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

Publications: click on link for abstract and link to article

Quantitative ornithology with a marine radar. Methods in Ecology and Evolution. 2016. Diel variation in  Gulf of Mexico Sound Scattering Layers.Deep-Sea Research I. 2016. Energy gain by migrating humpback whales.
Polar Biology. 2016.

Wildfire smoke changes zooplankton distribution. GRL. 2016. Effects of UV radiation on lakes and their ecosystem services. FEE. 2016. Measuring lake zooplankton with 710kHz echosounder. L&O: Methods. 2016. Effect of prey on foraging Australian humpback whales. MEPS. 2015. Material properties of hake, squid, and myctophids. JASA. 2015.
Material properties of Northeast Pacific zooplankton. ICES Journal of Marine Science. 2014 Ecosystem response to a temporary sea ice retreat in the Bering Sea: Winter 2009. Progress in Oceanography. 2013. 

A distorted wave Born approximation target strength model for Bering Sea euphausiids. ICES J. Mar. Sci. 2013.

Counting critters in the sea using active acoustics. Acoustics Today. 2012. [lay language article] Developing an acoustic survey of euphausiids to understand trophic interactions in the Bering Sea ecosystem.  Deep Sea Research II. 2012.
Dangerous dining: surface foraging of North Atlantic right whales increases risk of vessel collisions. Biology Letters. 2012.

Material properties of euphausiids and other zooplankton from
the Bering Sea. J. Acoust. Soc. Am. 2010.

Abundance and distribution of Antarctic krill (Euphausia superba) nearshore of Cape Shirreff, Livingston Island, Antarctica, during six austral summers between 2000 and 2007. Can. J. Fish. Aq. Sci. 2010. Three-dimensional
observations of swarms of
Antarctic krill (Euphausia
superba) made using a
multi-beam echosounder.
Deep Sea Research II. 2010.
Variability in the density and sound-speed of coastal zooplankton and nekton. ICES J. Mar. Sci. 2009.
Multibeam echosounder observations reveal interactions between Antarctic krill and air-breathing predators. Marine Ecology Progress Series. 2009. Submesoscale distribution of Antarctic krill and its avian and pinniped predators before and after a near gale. Marine Biology. 2009. Accounting for biological and physical sources of acoustic backscatter improves estimates of zooplankton biomass. Can. J. Fish. Aq. Sci. 2008.  Density and sound speed of two gelatinous zooplankton. J. Acoust. Soc. Am. 2007 Use of ADCP to measure estuarine bottom and SAV characteristics. Est. Coast. Shelf Sci. 2007.
West Falmouth oil spill, Env. Forensics, 2005 Zooplankton west of Antarctic peninsula, Deep Sea Res. II, 2004  Zooplankton in Ligurian Sea Part II, J. Plankton Res. 2004 Zooplankton in Ligurian Sea Part I, J. Plankton Res. 2004 Biological and physical scattering in an internal wave, ICES J. Mar. Sci. 2003
BIOMAPER-II, IEEE J. Oceanic. Eng. 2002 Effect of animal orientation, IEEE J. Ocean. Eng. 2002 In situ TS of siphonophores, ICES J. Mar. Sci. 2001 Scattering by benthic and planktonic shells; JASA 2000 Near-bottom boundary layer; CSR 1997
Please feel free to contact me if you would like a reprint of any of these papers.

S.S. Urmy and J.D. Warren. 2016. Quantitative ornithology with a commercial marine radar: standard-target calibration, target detection and tracking, and measurement of echoes from individuals and flocks. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12699 [.pdf]

Summary: 1. Marine surveillance radars are commonly used for radar ornithology, but they are rarely calibrated. This prevents them from measuring the radar cross-sections (RCS) of the birds under study. Furthermore, if the birds are aggregated too closely for the radar to resolve them individually, the bulk volume reflectivity cannot be translated into a numerical density. 2. We calibrated a commercial off-the-shelf marine radar, using a standard spherical target of known RCS. Once calibrated, the radar was used to measure the RCS of common and roseate terns (Sterna hirundo L. and Sterna dougallii Montagu) tracked from a land-based installation at their breeding colony on Great Gull Island, NY, USA. We also integrated echoes from flocks of terns, comparing these total flock cross-sections with visual counts from photos taken at the same time as the radar measurements. 3. The radar's calibration parameters were determined with 1% error. RCS measurements made after calibration were expected to be accurate within ±2 dB. Mean tern RCS was estimated at −28 dB relative to one square meter (dBsm), agreeing in magnitude with a simple theoretical model. RCS was 3–4 dB higher when birds’ aspect angles were broadside to the radar beam compared with head- or tail-on. Integrated flock cross-section was linearly related to the number of birds. The slope of this line, an independent estimate of RCS, was −32 dBsm, within an order of magnitude of the estimate from individual birds, and near the middle of the frequency distribution of RCS values. 4. These results indicate that a calibrated marine radar can count the birds in an aggregation via echo integration. Field calibration of marine radars is practical, enables useful measurements, and should be done more often.

M. D'elia, J.D. Warren, I. Rodriguez-Pinto, T.T. Sutton, A. Cook, K.M. Boswell. 2016. Diel variation in the vertical distribution of deep-water scattering layers in the Gulf of Mexico. Deep-Sea Research I. 115:91-102. doi:10.1016/j.dsr.2016.05.014 [.pdf]

Sound scattering layers (SSLs) are important components of oceanic ecosystems with ubiquitous dis- tribution throughout the world's oceans. This vertical movement is an important mechanism for ex- changing organic matter from the surface to the deep ocean, as many of the organisms comprising SSLs serve as prey resources for linking the lower trophic levels to larger predators. Variations in abundance and taxonomic composition of mesopelagic organisms were quantified using repeated discrete net sampling and acoustics over a 30-h survey, performed during 26–27 June 2011 at single site (27°28’51”N and 88°27’54”W) in the northern Gulf of Mexico. We acoustically classified the mesopelagic SSL into four broad taxonomic categories, crustacean and small non-swimbladdered fish (CSNSBF), large non-swim- bladdered fish (LNSBF), swimbladdered fish (SBF) and unclassified and we quantified the abundance of mesopelagic organisms over three discrete depth intervals; epipelagic (0–200 m); upper mesopelagic (200–600 m) and lower mesopelagic (600–1000 m). Irrespective of the acoustic categories at dusk part of the acoustic energy redistributed from the mesopelagic into the upper epipelagic (shallower than 100 m) remaining however below the thermocline depth. At night higher variability in species composition was observed between 100 and 200 m suggested that a redistribution of organisms may also occur within the upper portion of the water column. Along the upper mesopelagic backscatter spectra from CSNSBF migrated between 400 and 460 m while spectra from the other categories moved to shallower depths (300 and 350 m), resulting in habitat separation from CSNSBF. Relatively small vertical changes in both acoustic backscatter and center of mass metrics of the deep mesopelagic were observed for CNSBF and LNSBF suggesting that these animals may be tightly connected to deeper (below 1000 m) mesopelagic habitats, and do not routinely migrate into the epipelagic.

K. Owen, A. S. Kavanagh, J.D. Warren, M.J. Noad, D. Donnelly, A.W. Goldizen, R.A. Dunlop. 2016. Potential energe gain by whales outside fo the Antarctic: prey preferences and consumption rates of migrating humpback whales (Megaptera Novaeangliae). Polar Biology. doi:10.1007/s00300-016-1951-9 [.pdf]

The humpback whale (Megaptera novaeangliae) makes annual migrations from Antarctic feeding grounds to tropical breeding grounds. The extent to which it feeds during migration is unknown, but thought to be very low. Whether an animal feeds during migration is likely dependent on prey availability and on the ease with which it can capture the available prey. This study used digital tags (DTAGs) and concurrent prey sampling to measure how changes in the depth and type of prey influenced the lunge feeding rates and the amount of energy consumed by migrating humpback whales. Whales targeting krill lunged at significantly higher rates than whales targeting fish; however, the depth of the prey did not influence lunge rate. The observed lunge rates when feeding on krill, to the best of our knowledge, are higher than any previously reported rates of whales feeding. Estimates of the energetic content of the prey ingested revealed that whales may consume between 1.2 and 3.4 times their daily energy requirements per day while feeding on krill during migration, but less when feeding on fish. This suggests that whales may begin to restock energy supplies prior to reaching the Antarctic. Determining how often this high rate of energy intake occurs along the migratory route will assist with understanding the contribution of migratory energy intake to annual energy budgets.

S.S. Urmy, C.E. Williamson, T.H. Leach, S.G. Schladow, E.P. Overholt, J.D. Warren. 2016.Vertical redistribution of zooplankton in an oligotrophic lake associated with reduction in ultraviolet radiation by wildfire smoke. Geophysical Research Letters. doi:10.1002/2016GL068533 [.pdf]

We used a natural experiment to test whether wildfire smoke induced changes in the vertical distribution of zooplankton in Lake Tahoe by decreasing incident ultraviolet radiation (UV). Fires have a variety of effects on aquatic ecosystems, but these impacts are poorly understood and have rarely been observed directly. UV is an important driver of zooplankton vertical migration, and wildfires may alter it over large spatial scales. We measured UV irradiance and the distribution of zooplankton on two successive days. On one day, smoke haze from a nearby wildfire reduced incident UV radiation by up to 9%, but not irradiance in the visible spectrum. Zooplankton responded by positioning themselves, on average, 4.1 m shallower in the lake. While a limited data set such as this requires cautious interpretation, our results suggest that smoke from wildfires can change the UV environment and distribution of zooplankton. This process may be important in drought-prone regions with increasingly frequent wildfires, and globally due to widespread biomass burning.

C.E. Williamson, E.P. Overholt, J.A. Brentrup, R.M. Pilla, T.H. Leach, S.G. Schladow, J.D. Warren, S.S. Urmy, S. Sadro, S. Chandra, P.J. Neale. 2016. Sentinel responses to droughts, wildfires, and floods: Ultraviolet radiation and the consequences for lakes and their ecosystem services. Frontiers in Ecology and Environment. 14(2): 102-109. doi:10.1002/fee.1228 [.pdf]

Environmental drivers such as climate change are responsible for extreme events that are critically altering freshwater resources across the planet. In the continental US, these events range from increases in the frequency and duration of droughts and wildfires in the West, to increasing precipitation and floods that are turning lakes and reservoirs brown in the East. Such events transform and transport organic carbon in ways that affect the exposure of ecosystems to ultraviolet (UV) radiation and visible light, with important implications for ecosystem services. Organic matter dissolved in storm runoff or released as black carbon in smoke selectively reduces UV radiation exposure. In contrast, droughts generally increase water transparency, so that UV radiation and visible light penetrate to greater depths. These shifts in water transparency alter the potential for solar disinfection of waterborne parasites, the production of carcinogenic disinfection byproducts in drinking water, and the vertical distribution of zooplankton that are a critical link in aquatic food webs.

J.D. Warren, T.H. Leach, and C.E. Williamson. 2016. Measuring the distribution, abundance, and biovolume of zooplankton in an oligotrophic freshwater lake with a 710 kHz scientific echosounder. Limnology & Oceanography: Methods. doi:10.1002/lom3.10084 [.pdf]

Acoustic surveys of the distribution and abundance of freshwater zooplankton were conducted in Lake Giles, an oligotrophic freshwater lake. Volume backscatter data from a 710 kHz scientific echosounder were converted to high-resolution spatial and temporal numerical density estimates of small zooplankton. Vertical net tows of a 153 μm mesh closing bongo net at multiple depth intervals provided both identification of the types and sizes (0.5–1.5 mm length) of crustacean zooplankton present in the lake as well as an independent measurement of zooplankton numerical density. Net and acoustic estimates of zooplankton abundance, biovolume, and distribution were very similar. The improved resolution of the high-frequency acoustic sampling provides insight into several aspects of freshwater zooplankton ecology including: separation of migrating and non-migrating zooplankton, high resolution measurements of in situ zooplankton biovolume, calculation of in situ vertical velocities of migrating zooplankton, and fine-scale (sub-meter) horizontal and vertical zooplankton distribution during daytime, nighttime, and vertical migration events. These methods allow for more detailed and accurate estimates of zooplankton distribution than traditional net sampling methods can provide, including determining the total abundance of organisms within a specific habitat. They also provide higher resolution data in both space and time of smaller zooplankton taxa than have been measured previously in freshwater ecosystems.

K. Owen, J.D. Warren, M.J. Noad, D. Donnelly, A.W. Goldizen, and R.A. Dunlop. (2015) The effect of prey type on the fine-scale feeding behaviour of migrating east Australian humpback whales. Marine Ecology Progress Series. 541: 231-244 doi:10.3354/meps11551 [.pdf]

For terrestrial migrants, feeding at migratory stopover sites is important, with prey quality linked to future survival and reproductive success. In contrast, the importance of this behaviour to marine species is unknown. The humpback whale Megaptera novaeangliae is a marine migrant that is thought to fast while migrating; however, recent studies suggest that feeding may occur during this time. The aims of this study were to determine how the prey type available on a migratory route off Eden, New South Wales, Australia, influenced whether whales fed or not, and to study the fine-scale behaviour of the whales. Digital acoustic recording tags (DTAGs) and focal follows were used to record whale behaviour. A larger proportion of groups were determined to be feeding when krill was observed at the surface. Whales encountering fish
spent a small percentage (28%) of time feeding, behaving similarly to non-feeding whales on migration, with small groups, a higher proportion of males sampled, and relatively straight tracks. In contrast, whales encountering surface swarms of krill spent significantly more time feeding (92%) and behaved similarly to whales on feeding grounds, with larger groups, more females sampled, and tracks with high turning angles. Therefore, changes in the available prey type influenced the amount of time spent feeding and the social dynamics of groups. Given the link between the amount of feeding completed on migration and the future survival and reproductive success of individuals in terrestrial species, the impact of such fluctuations on marine species such as the humpback whale deserves more attention.

K.N. Becker and J.D. Warren. 2015. Material properties of Pacific hake, Humboldt squid, and two species of myctophids in the California Current. Journal of the Acoustical Society of America. 137(5): 2522-2532. doi: 10.1121/1.4919308. [.pdf]

Material properties of the flesh from three fish species (Merluccius productus, Symbolophorus californiensis,
and Diaphus theta), and several body parts of the Humboldt squid (Dosidicus gigas) collected
from the California Current ecosystem were measured. The density contrast relative to
seawater varied within and among taxa for fish flesh (0.9919 - 1.036), squid soft body parts (mantle,
arms, tentacle, braincase, eyes; 1.009 - 1.057), and squid hard body parts (beak and pen;
1.085 - 1.459). Effects of animal length and environmental conditions on nekton density contrast
were investigated. The sound speed contrast relative to seawater varied within and among taxa for
fish flesh (0.986 - 1.027) and Humboldt squid mantle and braincase (0.937 - 1.028). Material properties
in this study are similar to values from previous studies on species with similar life histories.
In general, the sound speed and density of soft body parts of fish and squid were 1%-3% and
1%-6%, respectively, greater than the surrounding seawater. Hard parts of the squid were significantly
more dense (6%-46%) than seawater. The material properties reported here can be used
to improve target strength estimates from acoustic scattering models, which could increase the
accuracy of biomass estimates from acoustic surveys for these nekton.

K.N. Becker and J.D. Warren. 2014. Material properties of Northeast Pacific zooplankton. ICES Journal of Marine Science.  71(9): 2550-2563 doi: 10.1093/icesjms/fsu109. [.pdf]

We measured the density and sound speed contrasts relative to seawater of Northeast Pacific zooplankton. The density contrast (g) was measured for euphausiids, decapods (Sergestes similis), amphipods (Primno macropa, Phronima sp., and Hyperiid spp.), siphonophore bracts, chaetognaths, larval fish, crab megalopae, larval squid, and medusae. Morphometric data (length, width, and height) were collected for these taxa. Density contrasts varied within and between zooplankton taxa. The mean and standard deviation (s.d.) for euphausiid density contrast were 1.059 ± 0.009. Relationships between zooplankton density contrast and morphometric measurements, geographic location, and environmental conditions were investigated. Site had a significant effect on euphausiid density contrast. Density contrasts of euphausiids collected in the same geographic area ∼4–10 d apart were significantly higher (p < 0.001). Sound speed contrast (h) was measured for euphausiids and pelagic decapods (S. similis) and it varied between taxa. The mean and s.d. for euphausiid sound speed were 1.019 ± 0.009. Euphausiid mass was calculated from measured density and volume, and a relationship between euphausiid mass and length was produced. We determined that euphausiid volume could be accurately estimated from two-dimensional measurements of animal body shape, and that biomass (or biovolume) could be accurately calculated from digital photographs of animals. Data from this study can improve the accuracy of theoretical acoustic scattering models for these taxa, resulting in more accurate estimates of zooplankton biomass in this region.

J.L. Miksis-Olds, P.J. Stabeno, J.M. Napp, A.I. Pinchuk, J.A. Nystuen, J.D. Warren, S.L. Denes. 2013. Ecosystem response to a temporary sea ice retreat in the Bering Sea: Winter 2009. Progress in Oceanography. 111: 38-51. doi: 10.1016/j.pocean.2012.10.010. [.pdf]

Adding acoustic systems onto ocean moorings and observatories provides additional data to more fully document ecosystem responses to environmental perturbations. A passive acoustic recorder and three-frequency echosounder system were integrated into a biophysical mooring on the central eastern Bering Sea continental shelf. An unexpected, transient, mid-winter retreat of the seasonal sea ice was observed over the mooring for a 2-week period in March 2009. Interpretation of the passive acoustic data provided information about sea ice conditions and included the detection and identification of vocalizing marine mammals, while the acoustic backscatter provided information on relative zooplankton and fish abundance before, during, and after the retreat. Hydrographic data confirmed the acoustic signal was associated with changing surface ice conditions, and the combined information from the biophysical mooring sensors revealed changes in winter trophic level dynamics during the retreat, which would have otherwise been undetected by traditional ship-based observations. Changes in the acoustic environment, zooplankton dynamics, and acoustic detection of marine mammals were observed amidst a physically stable and uniform water column with no indication of a phytoplankton bloom. These data demonstrate the value of acoustic technologies to monitor changing ecosystems dynamics in remote and hazardous locations.

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 [.pdf]

An invited paper for the lay-language magazine for the Acoustical Society of America as part of a special issue on Remote Sensing of Animals.

Joy N. Smith, P.H. Ressler, J.D. Warren. 2013. A distorted wave Born approximation target strength model for Bering Sea euphausiids. ICES Journal of Marine Science. 70(1): 204-214. doi: 10.1093/icesjms/fss140 [.pdf]

Acoustic surveys monitor euphausiid populations in the Bering Sea because of their importance as prey for walleye pollock and other organisms. Various scattering models exist to convert acoustic backscatter data to estimates of euphausiid numerical density or biomass, but a target strength (TS) model specific to Bering Sea euphausiids has not been available. This study parameterized a distorted wave Born approximation (DWBA) scattering model using physical (length and body shape) and material (density contrast, g, and sound speed contrast, h) properties measured from live euphausiids. All model parameters (length, shape, material properties, orientation) were evaluated for their effect on predicted TS. A polynomial function was used to describe animal shape and produced smaller TS estimates compared to a taper function, as is traditionally used in DWBA scattering models of euphausiids. Animal length was positively correlated with TS, but variations in other parameters (including material properties and orientation) also produced large changes in TS. Large differences in TS between estimates calculated using measured versus literature material property values caused large variations in acoustic estimates of euphausiid numerical densities (animals m23) which emphasizes the importance of collecting site-specific g and h measurements when possible.

P.H. Ressler, A. De Robertis, J.D. Warren, Joy N. Smith, S. Kotwicki. 2012. Developing an acoustic survey of euphausiids to understand trophic interactions in the Bering Sea ecosystem. Deep Sea Research II. 65-70: 184-195. doi: 10.1016/j.dsr2.2012.02.015 [.pdf]

Euphausiids (principally Thysanoessa spp.) are a key group of organisms in the Bering Sea ecosystem, linking production at lower trophic levels to top predators and important commercial fish stocks such  as walleye pollock (Theragra chalcogramma). Here, we combine multifrequency acoustic survey methods, physics-based models of euphausiid backscatter, and net sampling to provide a means of monitoring the status and trends of euphausiid standing stock biomass on the Bering Sea shelf. Observations made using this approach during six summers (2004 and 2006–2010) indicate that  standing stocks of euphausiids and pollock were inversely correlated over time as well as in space across the continental shelf. First-order calculations show that when pollock abundance was at its peak during these years, the pollock stock could have consumed 10–87% of the euphausiid standing stock between May and September. We hypothesize that predation by pollock is a significant top-down control on euphausiid standing stock in this system.

S.E. Parks, J.D. Warren, K. Stamieszkin, C.A. Mayo, D. Wiley. 2012. Dangerous dining: surface foraging of North Atlantic right whales increases risk of vessel collisions. Biology Letters. 8(1): 57-60. doi: 10.1098/rsbl.2011.0578 [.pdf]

North Atlantic right whales are critically endangered and, despite international protection from whaling, significant numbers die from collisions with ships. Large groups of right whales migrate to the coastal waters of New England during the late winter and early spring to feed in an area with large numbers of vessels. North Atlantic right whales have the largest per capita record of vessel strikes of any large whale population in the world. Right whale feeding behaviour in Cape Cod Bay (CCB) probably contributes to risk of collisions with ships. In this study, feeding right whales tagged with archival suction cup tags spent the majority of their time just below the water’s surface where they cannot be seen but are shallow enough to be vulnerable to ship strike. Habitat surveys show that large patches of right whale prey are common in the upper 5 m of the water column in CCB during spring. These results indicate that the typical spring-time foraging ecology of right whales may contribute to their high level of mortality from vessel collisions. The results of this study suggest that remote acoustic detection of prey aggregations may be a useful supplement to the management and conservation of right whales.

J.N. Smith, P.H. Ressler, and J.D. Warren. 2010. Material properties of euphausiids and other zooplankton from the Bering Sea. Journal of the Acoustical Society of America. 128(5): 2664-2680. doi: 10.1121/1.3488673 [.pdf]

Acoustic assessment of Bering Sea euphausiids and their predators can provide useful data for ecosystem studies if the acoustic scattering characteristics of these animals are known. The amount of acoustic energy that is scattered by different marine zooplankton taxa is strongly affected by the contrast of the animal’s density g and sound speed h with the surrounding seawater. Density and sound speed contrast were measured in the Bering Sea during the summer of 2008 for several different zooplankton and nekton taxa including: euphausiids (Thysanoessa inermis, Thysanoessa raschii, and Thysanoessa spinifera), copepods, amphipods, chaetognaths, gastropods, fish larvae, jellyfish, and squid. Density contrast values varied between different taxa as well as between individual animals within the same species. Sound speed contrast was measured for monospecific groups of animals and differences were found among taxa. The range, mean, and standard deviation of g and h for all euphausiid species were: g = 1.001– 1.041; 1.018; 0.009 and h = 0.990– 1.017; 1.006; 0.008. Changes in the relationship between euphausiid material properties and animal length, seawater temperature, seawater density, and geographic location were also evaluated. Results suggest that environmental conditions at different sample locations led to significant differences in animal density and material properties.

J.D. Warren and D.A. Demer. 2010. Abundance and distribution of Antarctic krill (Euphausia superba) nearshore of Cape Shirreff, Livingston Island, Antarctica, during six austral summers between 2000 and 2007. Canadian Journal of Fisheries and Aquatic Sciences. 67(7): 1159-1170. doi:10.1139/F10-042 [.pdf]

Abundance and distribution of Antarctic krill (Euphausia superba) in the nearshore waters north of Livingston Island, Antarctica, were characterized from six small-boat surveys conducted in late January or early February from 2000 to 2007. The first three surveys (2000, 2002, 2004) were conducted using a 120 kHz split-beam echosounder to measure water column acoustic backscatter. The last three surveys (2005–2007) were conducted using 38 kHz and 200 kHz single-beam echosounders. A portion of the acoustic backscatter was attributed to Antarctic krill based on the results of net tows, underwater video observations, and a multiple-frequency acoustic classification algorithm. The annual mean krill biomass density in the survey area ranged from 11 to 84 g·m–2. Results are compared with the western Scotia Sea area of the US Antarctic Marine Living Resources (AMLR) program’s acoustic surveys of krill biomass density for the same years. Nearshore krill biomass densities were significantly larger (t test, p < 0.05), more stable, and the coefficients of variation were smaller than the much larger AMLR surveys. Increased competition between seals, penguins, and humans for the nearshore krill resource, especially during the austral summer months, could impact the recruitment success of these land-based krill predators. Implications of nearshore krill biomass on small-scale management units are discussed.

M.J. Cox, J.D. Warren, D.A. Demer, G.R. Cutter, and A.S. Brierley. 2010. Three-dimensional observations of swarms of Antarctic krill (Euphausia superba) made using a multi-beam echosounder. Deep Sea Research II. doi:10.1016/j.dsr2.2009.10.003 [.pdf]

Antarctic krill (Euphausia superba) aggregate in dense swarms. Previous investigations of krill swarms
have used conventional single- or split-beam echosounders that, with post-processing, provide a two-
dimensional (2-D) view of the water column, leaving the third dimension to be inferred. We used a
multi-beam echosounder system (SM20, 200kHz, Kongsberg Mesotech Ltd, Canada) from an inflatable
boat (length=5.5m) to sample water-column backscatter, particularly krill swarms, directly in 2-D and,
with post-processing, to provide a three dimensional (3-D) view of entire krill swarms. The study took
place over six days(2–8 February 2006) in the vicinity of Livingston Island, South Shetland Islands,
Antarctica (62.41S, 60.71W). An automatic 3-D aggregation detection algorithm resolved 1006 krill
swarms from the survey data. Principal component analyses indicated that swarm morphology metrics
such as length, surface area and volume accounted for the largest between swarm variance, followed by
echo energy, and finally swarm geographic location. Swarms did not form basic cylindrical or spherical
shapes, but had quite consistent surface area to volume ratios of 3.3 m. Swarms were spatially
segregated, with larger sizes (mean north-south length = 276 m, at least double that of two other swarm
classifications), found to the northwest of the survey area.The apparent clustering of swarm types
suggests that krill biomass surveys and ecosystem investigations may require stratified survey design,
in response to varying 3-D swarm morphology, variation that may be driven in turn by environmental
characteristics such as bathymetry.

K.A. Forman and J.D. Warren. 2009. Variability in the density and sound-speed of coastal zooplankton and nekton. ICES Journal of Marine Science. doi: 10.1093/icesjms/fsp217 [.pdf]

Acoustic sampling techniques provide an advantage over traditional net-sampling by increasing scientific ability to survey a large area in a relatively short period, as well as providing higher-resolution data in the vertical and horizontal dimensions. To convert acoustic data into measures of biological organisms, physics-based scattering models are often used. Such models use several parameters to predict the amount of sound scattered by a fluid-like or weakly scattering animal. Two important input parameters are the density (g) and sound-speed (h) contrasts of the animal and the surrounding seawater. The density and sound-speed contrasts were measured for coastal zooplankton and nekton species including shrimps (Palaemonetes pugio and Crangon septemspinosa), fish (Fundulus majalis and Fundulus heteroclitus), and polychaetes (Nereis succinea and Glycera americana) along with multiple physiological and environmental variables. Factors such as animal size, feeding status, fecundity, gender, and maturity caused variations in g. The variations in g observed for these animals could lead to large differences (or uncertainties) in abundance estimates based on acoustic scattering models and field-collected backscatter data. It may be important to use a range of values for g and h in the acoustic scattering models used to convert acoustic data into estimates of the abundance of marine organisms.

M.J. Cox, D.A. Demer, J.D. Warren, G.R. Cutter, and A.S. Brierley. 2009. Multibeam echosounder observations reveal interactions between Antarctic krill and air-breathing predators Marine Ecology Progress Series 378: 199-209. doi: 10.3354/meps07795 [.pdf]

A multibeam echosounder (MBE) was deployed on an inflatable boat (length = 5.5 m) to observe swarms of Antarctic krill Euphausia superba in the nearshore environment off Livingston Island, South Shetland Islands, Antarctica. Visual observations of air-breathing predators, including penguins and fur seals, were made from the boat at the same time. MBEs extend the 2-dimensional acoustic observations that can be made with conventional vertical echosounders to 3 dimensions, enabling direct observation of the surface areas and volumes of entire krill swarms. Krill swarms exhibited a wide range of various size metrics (e.g. height, length and width) but only a narrow range of surface-area-to-volume ratios or ‘roughnesses’, suggesting that krill adopt a consistent group behavior to maintain swarm shape. The variation in R was investigated using generalized additive models (GAMs). GAMs indicated that the presence of air-breathing predators influenced swarm shape (R decreased as the range to predators decreased, and the swarms became more spherical), as did swarm nearest-neighbor distance (R decreased with increasing distance) and swarm position in the water column (R decreased in the upper 70% of the water column). Therefore, swarm shape appears to be influenced by a combination of behavioral responses to predator presence and environmental variables. MBEs have the potential to contribute much to studies of krill, and can provide data to improve our understanding of the behavior of krill in situ.

J. D. Warren, J.A. Santora, and D.A. Demer. 2009. Submesoscale distribution of Antarctic krill and its avian and pinniped predators before and after a near galeMarine Biology 156: 479-491. doi: 10.1007/s00227-008-1102-0 [.pdf]

We conducted two ship-based surveys of the nearshore ecosystem north of Livingston Island, Antarctica during 2–10 February 2005. Between the two surveys, a low-pressure system (963 mbar) passed through the area providing the opportunity to measure ecosystem parameters before and after a near gale. A ship-based multiple-frequency acoustic-backscatter survey was used to assess the distribution and relative abundance of Antarctic krill (Euphausia superba). Net tows, hydrographic profiles, and meteorological data were collected to measure biological and physical processes that might affect the krill population. During the survey, the distribution and behavior of several krill predators [chinstrap penguins (Pygoscelis antarctica), cape petrels (Daption capense), and Antarctic fur seals (Arctocephalus gazella)] were measured from the vessel by visual observations. The survey encompassed an area of roughly 2,500 km2, containing two submarine canyons with one to the west and one to the east of Cape Shirreff, which had different abundances of krill and predators. Several aspects of the nearshore ecosystem changed after the near gale including: hydrography of the upper 100 m of the water column, phytoplankton biomass, the abundance and distribution of krill, and the distribution of some krill predators. Differences in these parameters were also measured between the two canyons. These changes in the physical and biological environment during the survey period are quantified and show that the ecosystem exhibited significant changes over relatively short spatial (tens of kilometers) and time (tens of hours) scales.

J. D. Warren and P. H. Wiebe. 2008. Accounting for biological and physical sources of acoustic backscatter improves estimates of zooplankton biomass. Canadian journal of Fisheries and Aquatic Sciences 65: 1321-1333. doi:10.1139/F08-047 [.pdf]

To convert measurements of backscattered acoustic energy to estimates of abundance and taxonomic information about the zooplankton community, all of the scattering processes in the water column need to be identified and their scattering contributions quantified. Zooplankton populations in the eastern edge of Wilkinson Basin in the Gulf of Maine in the Northwest Atlantic were surveyed in October 1997. Net tow samples at different depths, temperature and salinity profiles, and multiple frequency acoustic backscatter measurements from the upper 200 m of the water column were collected. Zooplankton samples were identified, enumerated, and measured. Temperature and salinity profiles were used to estimate the amount of turbulent microstructure in the water column. These data sets were used with theoretical acoustic scattering models to calculate the contributions of both biological and physical scatterers to the overall measured scattering level. The output of these predictions shows that the dominant source of acoustic backscatter varies with depth and acoustic frequency in this region. By quantifying the contributions from multiple scattering sources, acoustic backscatter becomes a better measure of net-collected zooplankton biomass.

The density and sound speed of two coastal, gelatinous zooplankton, Mnemiopsis leidyi (a ctenophore) and Cyanea capillata (lion's mane jellyfish), were measured. These parameters are important inputs to acoustic scattering models. Two different methods were used to measure the density of individual animals: one used a balance and graduated cylinder to determine the mass and displacement volume of the animal, the other varied the density of the solution the animal was immersed in. When the same animal was measured using both methods, density values were within 1% of each other. A travel-time difference method was used to measure the sound speed within the animals. The densities of both zooplankton slightly decreased as the animals increased in length, mass, and volume. The ratio of animal density and sound speed to the surrounding seawater (g and h, respectively) are reported for both animals. For Mnemiopsis leidyi ranging in length from 1 to 5  cm, the mean value (±standard deviation) of g and h were 1.009 (±0.004) and 1.007 (±0.001). For Cyanea capillata ranging in bell diameter from 2 to 11  cm, the mean value (±standard deviation) of g and single value of h were 1.009 (±0.004) and 1.0004. ©2007 Acoustical Society of America

The acoustic backscatter intensity signal from a high-frequency (600 kHz) Acoustic Doppler Current Profiler (ADCP) was used to categorize four different types of bottom habitat (sand, mud, sparse and dense vegetation) in a shallow-water estuary (Shinnecock Bay, NY, USA). A diver survey of the bay measured sediment and bottom vegetation characteristics at 85 sites within the bay. These data were used to groundtruth the acoustic data. Acoustic data were collected at four sites with known bottom types and used to develop an algorithm that could categorize the bottom type. The slope of the echo intensity profile close to the bottom was used to determine the bottom type and the relative numerical density (sparse or dense) of Submerged Aquatic Vegetation (SAV). In areas where eelgrass (Zostera marina) was the dominant SAV species, the intensity profile data were analyzed to measure the height of the vegetation canopy. An acoustic survey which categorized the bottom type of the bay was conducted from a small vessel. The percentage of sampled sites categorized as each bottom habitat type from the acoustic survey was similar to those obtained by the diver survey. These methods may provide a means to rapidly survey estuarine habitats and measure spatial and temporal variations in SAV populations, as well as changes in the height of the eelgrass canopy.

E. Peacock , R. Nelson, A. Solow, J. Warren, J. Baker and C. Reddy, 2005, The West Falmouth Oil Spill: ~100 Kg of Oil Found to Persist Decades Later , Environmental Forensics, 6(3): 273-281. [.pdf]

In order to investigate the long-term fate of petroleum hydrocarbons in salt marsh sediments in Wild Harbor (West Falmouth, MA) impacted by the Florida spill of 1969, 26 sediment cores were collected and analyzed for total petroleum hydrocarbons (TPH). The results from this effort indicate that the distribution of petroleum hydrocarbons is spatially heterogeneous, oil compounds are generally located at sediment depths of 4 to 20 cm in areas closest to the banks of the marsh, and ~ 100 kg of petroleum residues can be found to persist in intertidal sediments that were originally the most impacted.

G. L. Lawson, P. H. Wiebe, C. J. Ashjian, S. M. Gallager, C. S. Davis, and J. D. Warren, 2004, Acoustically-inferred zooplankton distribution in relation to hydrography west of the Antarctic Peninsula , Deep-Sea Research. Part II, 51(17-19): 2041-2072. [.pdf]

The relationship between the distribution of zooplankton, especially euphausiids (Euphausia and Thysanoessa spp.), and hydrographic regimes of the Western Antarctic Peninsula continental shelf in and around Marguerite Bay was studied as part of the Southern Ocean GLOBEC program. Surveys were conducted from the RVIB N. B. Palmer in austral fall (April-June) and winter (July- August) of 2001. Acoustic, video, and environmental data were collected along 13 transect lines running across the shelf and perpendicular to the Western Antarctic Peninsula coastline, between 65°S and 70°S. Depth-stratified net tows conducted at selected locations provided ground-truthing for acoustic observations. In fall, acoustic volume backscattering strength at 120 kHz was greatest in the southern reaches of the survey area and inside Marguerite Bay, suggestive of high zooplankton and micronekton biomass in these regions. Vertically, highest backscattering was in the 150-450 m depth range, associated with modified Circumpolar Deep Water (CDW). The two deep troughs that intersect the shelf break were characterized by reduced backscattering, similar to levels observed off-shelf and indicative of lower zooplankton biomass in recent intrusions of CDW onto the continental shelf. Estimates of dynamic height suggested that geostrophic circulation likely caused both along- and across-shelf transport of zooplankton. By winter, scattering had decreased by an order of magnitude (10 dB) in the upper 300 m of the water column in most areas, and high backscattering levels were found primarily in a deep (›300 m) scattering layer present close to the bottom. The seasonal decrease is potentially explained by advection of zooplankton, vertical and horizontal movements, and mortality. Predictions of expected backscattering levels based on net samples suggested that large euphausiids were the dominant source of backscattering only at very particular locations and depths, and that copepods, siphonophores, and pteropods were more important in many locations.

J. D. Warren , D. A. Demer, D. E. McGehee, R. Di Mento and J. F. Borsani, 2004, Zooplankton in the Ligurian Sea: Part II. Exploration of their physical and biological forcing functions during summer 2000, Journal of Plankton Research, 26(12): 1409-1418. [.pdf]

A survey of the biological and physical oceanography of the Ligurian Sea was conducted in the late summer of 2000. Forty-one stations were sampled for nutrients, oxygen, fluorescence and hydrographic information. Acoustic backscatter measurements were used to estimate abundance of small (<5 mm) zooplankton biovolume versus depth and the distribution of northern krill, Meganyctiphanes norvegica. Net-tow and underwater video data were collected to identify the zooplankton present. These data were used to analyze the Ligurian Sea ecosystem for physical and biological linkages that control zooplankton abundance and distribution. Results are compared with those from a similar study conducted in 1999. Hydrographic sampling showed a dome of dense water in the southwestern middle of the basin. The highest chlorophyll a (Chl a) concentrations were measured in this area, while small zooplankton biovolume was evenly distributed throughout the survey. Integrated values of Chl a and small zooplankton biovolume in 2000 were greater than in 1999. Meganyctiphanes norvegica, siphonophores and salps were the dominant components of the macrozooplankton population in the upper 200 m. In the sampled depth strata, siphonophore abundance did not change during the day, while M. norvegica were only caught at night. Acoustic backscatter data show that higher densities of M. norvegica occurred in deeper water and in the western and southwestern areas of the Ligurian Sea.

D. E. McGehee, D. A. Demer, and J. D. Warren, 2004, Zooplankton in the Ligurian Sea: Part I. Characterization of their dispersion, relative abundance and environment during summer 1999, Journal of Plankton Research, 26(12): 1409-1418. [.pdf]

The distributions of temperature, salinity, chlorophyll and zooplankton were measured in the Ligurian Sea, north of Corsica, in August 1999. To characterize the physical environment, hydrographic and fluorometric profiles were collected. A net and two acoustic systems were used to measure the distribution of small (<5 mm) and large (>5 mm) zooplankton. Highest chlorophyll values were strongly associated with a dome of dense water in the center of the Ligurian Basin. Small zooplankton (copepods and smaller), in contrast, appeared to be associated with the periphery of the basin and were negatively correlated with chlorophyll. Large zooplankton were not correlated with either chlorophyll or small zooplankton. Large zooplankton migrated vertically hundreds of meters every night, while small zooplankton did not appear to migrate much. The physical observations were consistent with (i) a well-documented geostrophically driven cyclonic coastal current (the Ligurian Current) fed by sources in the Algerian Basin and Tyrrhenian Sea and (ii) upwelling in the central Ligurian Basin. Large zooplankton, being strong vertical migrators, were potentially insulated from the effects of the currents and therefore stayed resident.

J. D. Warren, T. K. Stanton, P. H. Wiebe, and H. E. Seim, 2003, Inference of biological and physical parameters in an internal wave using multiple-frequency, acoustic-scattering data, ICES Journal of Marine Science, 60(5): 1033-1046. [.pdf]

High-frequency sound (>10 kHz) is scattered in the ocean by many different processes. In the water column, marine organisms are often assumed to be the primary source of acoustic backscatter. Recent field experiments and theoretical work suggest that the temperature and salinity microstructure in some oceanic regions could cause acoustic scattering at levels comparable to that caused by marine life. Theoretical acoustic-scattering models predict that the scattering spectra for microstructure and organisms are distinguishable from each other over certain frequency ranges. A method that uses multiple-frequency acoustic data to exploit these differences has been developed, making it possible to discriminate between biological and physical sources of scattering under some conditions. This method has been applied to data collected in an internal wave in the Gulf of Maine. For regions of the internal wave in which the dominant source of scattering is either biological or physical in origin, it is possible to combine the acoustic-scattering data and temperature and salinity profiles with acoustic-scattering models to perform a least-squares inversion. Using this approach, it is possible to estimate the dissipation rate of turbulent kinetic energy for some regions of the internal wave, and the length and numerical abundance of the dominant biological scatterer, euphausiids, in others.

P. H. Wiebe, T. K. Stanton, C. H. Greene, M. C. Benfield, H. M. Sosik, T. C. Austin, J. D. Warren, and T. Hammar, 2002, BIOMAPER-II: An integrated instrument platform for coupled biological and physical measurements in coastal and oceanic regimes , IEEE Journal of Oceanic Engineering, 27(3): 700-716. [.pdf]

The BIo-Optical Multi-frequency Acoustical and Physical Environmental Recorder or BIOMAPER-II is a newly developed towed system capable of conducting quantitative surveys of the spatial distribution of coastal and oceanic plankton/nekton, near surface bubble fields, and turbulence, as well as field verification studies of theoretical plankton reverberation models. The system consists of a multi-frequency sonar (up-looking and down-looking pairs of transducers operating at five frequencies: 43, 120, 200, 420, and 1000 kHz), a video plankton recorder system (VPR), an environmental sensor system (CTD, fluorometer, transmissometer), and several other bio-optical sensors (down- and upwelling spectral radiometers, spectral attenuation, and backscattering, and absorption meters). The lower four acoustical frequencies utilize split beam technology and are able to make target strength and echo integration measurements. Also included are an electro-optic tow cable, a winch with slip rings, and a van which holds the electronic equipment for real-time data processing and analysis. The vehicle is capable of operating to a depth of 300 m at 4–6 kn, while near the surface it may be towed at speeds up to 10 kn. The system can be operated in a surface-towed down-looking mode, in a vertical oscillatory “tow-yo” mode, or in a subsurface up/down-looking horizontal mode. To enhance the performance and utility of BIOMAPER-II in high sea states, a winch, slack tensioner, and over-boarding J-frame assembly are integrated with the system for deployment and handling. Wire tension records and the power spectra demonstrated the substantial protection that the slack tensioner system provided against excessive shock loading of the cable and the vehicle in sea states that would otherwise prevent work. The scientific capability of the vehicle is illustrated with acoustic, environmental, and bio-optical data sets collected from the Gulf of Maine on cruises in 1997 and 1999.

J.D. Warren, T. K. Stanton, D. E. McGehee, and D. Chu, 2002, Effect of animal orientation on acoustic estimates of zooplankton properties, IEEE Journal of Oceanic Engineering, 27(1): 130-138. [.pdf]

It is well known that the behavior of zooplankton and, in particular, their orientation distribution dramatically affects the level of backscattered acoustic energy. As a result, interpretation of acoustic survey data in the ocean is subject to error. In order to quantify these effects, laboratory data from two important classes of animals were collected. The data involved broad-band (350-650 kHz) acoustic signals insonifying individual animals whose orientation was varied over the range 0°-360° in 1° increments. The animals were from two major anatomical groups: fluid-like (decapod shrimp; Palaemonetes vulgaris) and elastic-shelled (periwinkles; Littorina littorea). The data were analyzed both in the time domain (with pulse compression processing) and the frequency domain. Averages of the laboratory data over different orientation distributions illustrate the variability in average target strength that can be expected in the ocean environment. The average target strength of the shrimp varied by 3 dB when averaged over orientation distributions centered around broadside and end-on incidence. In addition, size estimates from pulse compression processing of the broad-band echoes were made for various orientation distributions for both the shrimp and periwinkles. These results show the necessity of animal orientation information for the proper interpretation of acoustic backscatter data.

J. D. Warren, T. K. Stanton, M. C. Benfield, P. H. Wiebe, D. Chu and M. Sutor, 2001, In situ measurements of acoustic target strengths of gas-bearing siphonophores, ICES Journal of Marine Science 58(4): 740-749. [.pdf]

Acoustic target strengths of free-swimming siphonophores were measured in situ at 24 and 120kHz from a remotely operated vehicle equipped with both acoustic transducers and a video camera. The transducers and camera were co-registered by aiming both instruments at the same volume of water and time-stamping the recorded data. The video system allowed us to search for and identify siphonophores, and verified whether individual animals were centered in, or near, the axis of the acoustic beams. A towed, down-looking acoustic survey system (operating at 120kHz) measured the target and volume scattering strengths of scattering layers, presumed to be dominated by siphonophores. Spatial density of the sound scatterers was estimated from survey data. Our results confirm that free-swimming physonect siphonophores have relatively high acoustical target strengths caused by a gas inclusion in the pneumatophore of each animal. A relatively small number of these animals can dominate the backscattering detected by acoustic surveys even though other taxa may dominate the plankton on a numerical or biomass basis. Siphonophore colonies are fragile and cannot be reliably censused with nets. Our estimates of siphonophore target strengths can improve the ability to use acoustics to quantitatively census siphonophores and other taxa possessing comparably-sized gas inclusions.

T. K. Stanton, D. Chu, P. H. Wiebe, R. L. Eastwood and J. D. Warren, 2000, Acoustic scattering by benthic and planktonic shelled animals , Journal of the Acoustical Society of America, 108(2): 535-550. [.pdf]

Acoustic backscattering measurements and associated scattering modeling were recently conducted on a type of benthic shelled animal that has a spiral form of shell (Littorina littorea). Benthic and planktonic shelled animals with this shape occur on the seafloor and in the water column, respectively, and can be a significant source of acoustic scattering in the ocean. Modeling of the scattering properties allows reverberation predictions to be made for sonar performance predictions as well as for detection and classification of animals for biological and ecological applications. The studies involved measurements over the frequency range 24 kHz to 1 MHz and all angles of orientation in as small as 1° increments. This substantial data set is quite revealing of the physics of the acoustic scattering by these complex shelled bodies and served as a basis for the modeling. Specifically, the resonance structure of the scattering was strongly dependent upon angle of orientation and could be traced to various types of rays (e.g., subsonic Lamb waves and rays entering the opercular opening). The data are analyzed in both the frequency and time domain (compressed pulse processing) so that dominant scattering mechanisms could be identified. Given the complexity of the animal body (irregular elastic shell with discontinuities), approximate scattering models are used with only the dominant scattering properties retained. Two models are applied to the data, both approximating the body as a deformed sphere: (1) an averaged form of the exact modal-series-based solution for the spherical shell, which is used to estimate the backscattering by a deformed shell averaged over all angles of orientation, and produces reasonably accurate predictions over all k1aesr (k1 is the acoustic wave number of the surrounding water and aesr is the equivalent spherical radius of the body), and (2) a ray-based formula which is used to estimate the scattering at fixed angle of orientation, but only for high k1aesr. The ray-based model is an extension of a model recently developed for the shelled zooplankton Limacina retroversa that has a shape similar to that of the Littorina littorea but swims through the water [Stanton et al., J. Acoust. Soc. Am. 103, 236–253 (1998b)]. Applications of remote detection and classification of the seafloor and water column in the presence of shelled animals are discussed. ©2000 Acoustical Society of America.

J.F. Lynch, J. D. Irish, T. F. Gross, P. L. Wiberg, A. E. Newhall, P. A. Traykovski and J. D. Warren, 1997, Acoustic measurements of the spatial and temporal structure of near-bottom boundary layer in the 1990-1991 STRESS experiment , Continental Shelf Research, 17: 1271-1295. [.pdf]

As part of the 1990–1991 Sediment TRansport Events on Shelves and Slopes (STRESS) experiment, a 5 MHz Acoustic BackScatter System (ABSS) was deployed in 90 m of water to measure vertical profiles of near-bottom suspended sediment concentration. By looking at the vertical profile of concentration from 0 to 50 cm above bottom (cmab) with 1 cm vertical resolution, the ABSS was able to examine the detailed structure of the bottom boundary layer created by combined wave and current stresses. The acoustic profiles clearly showed the wave-current boundary layer, which extends to (order) 10 cmab. The profiles also showed evidence of an "intermediate" boundary layer, also influenced by combined wave and current stresses, just above the wave-current boundary layer. This paper examines the boundary-layer structure by comparing acoustic data obtained by the authors to a 1-D eddy viscosity model formulation. Specifically, these data are compared to a simple extension of the Grant-Glenn-Madsen model formulation. Also of interest is the appearance of apparently 3-D "advective plume" structures in these data. This is an interesting feature in a site which was initially chosen to be a good example of (temporally averaged) 1-D bottom boundary-layer dynamics. Computer modeling and sector-scanning sonar images are presented to justify the plausibility of observing 3-D structure at the STRESS site.