A generalized baleen whale call detection and classification system

Author Posting. © Acoustical Society of America, 2011. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 129 (2011): 2889-2902, doi:10.1121/1.3562166.Passive acoustic monitoring allows the assessment of marine mammal occurrence and distribution at greater temporal and spatial scales than is now possible with traditional visual surveys. However, the large volume of acoustic data and the lengthy and laborious task of manually analyzing these data have hindered broad application of this technique. To overcome these limitations, a generalized automated detection and classification system (DCS) was developed to efficiently and accurately identify low-frequency baleen whale calls. The DCS (1) accounts for persistent narrowband and transient broadband noise, (2) characterizes temporal variation of dominant call frequencies via pitch-tracking, and (3) classifies calls based on attributes of the resulting pitch tracks using quadratic discriminant function analysis (QDFA). Automated detections of sei whale (Balaenoptera borealis) downsweep calls and North Atlantic right whale (Eubalaena glacialis) upcalls were evaluated using recordings collected in the southwestern Gulf of Maine during the spring seasons of 2006 and 2007. The accuracy of the DCS was similar to that of a human analyst: variability in differences between the DCS and an analyst was similar to that between independent analysts, and temporal variability in call rates was similar among the DCS and several analysts.Funding for the fieldwork was provided by the NOAA NEFSC, WHOI Ocean Life Institute, and the WHOI John E. and Anne W. Sawyer Endowed Fund. Development of the detection and classification system was supported by a grant from the Office of Naval Research

Temporal and spatial distributions of delphinid species in Massachusetts Bay (USA) using passive acoustics from ocean gliders

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Silva, T. L., Mooney, T. A., Sayigh, L. S., & Baumgartner, M. F. Temporal and spatial distributions of delphinid species in Massachusetts Bay (USA) using passive acoustics from ocean gliders. Marine Ecology Progress Series, 631, (2019): 1-17, doi:10.3354/meps13180.Knowledge about marine mammal habitat use is necessary for informing ecosystem-based management and mitigating human impacts. Massachusetts Bay is an important marine mammal foraging area in the Gulf of Maine and an area of substantial human activity, but delphinid habitat use is poorly understood. The goals of this work were to (1) document temporal and spatial occurrence of delphinid species in Massachusetts Bay using passive acoustic monitoring from ocean gliders and (2) explore the potential influences of environmental conditions on delphinid distributions. Gliders were deployed in late fall and early winter of 2014 and 2015-2016 and were equipped with a digital acoustic recorder and conductivity-temperature-depth instrument. Gliders surveyed an area of approximately 1000 km2. Delphinid whistles were detected on 93 of 128 (73%) deployment days. Animals were detected more often at night. Presence was consistent over 2 years, although detection rates showed annual and monthly variability. Spatial distribution differed between years, but most detections occurred close to Stellwagen Bank. Visual assessment of spectrograms suggests the presence of 2 species, Atlantic white-sided dolphins and common dolphins. The reoccurrence of 2 probable signature whistles over several weeks and consecutive winter seasons suggests prolonged occupancy during winter and possible annual site fidelity. These data show a consistent and frequent presence of delphinids near a known marine mammal foraging area (Stellwagen Bank) during late fall and winter and are a first step towards understanding both how odontocetes influence the Massachusetts Bay/Gulf of Maine ecosystem and how they may be impacted by human activities.We gratefully acknowledge the NOAA Northeast Fisheries Science Center, Stellwagen Bank National Marine Sanctuary, The Nature Conservancy, Massachusetts Division of Marine Fisheries, and the University of Massachusetts Dartmouth for their collaboration and support for this project. We thank Susan Parks, Julie Oswald, Sofie Van Parijs, and Danielle Cholewiak for helpful discussionsand sharing acoustic recordings for species comparisons. We are grateful to Ben Hodges for critical assistance with preparing, deploying, and recovering gliders. Thanks to Michael Thompson for assistance with spatial analysis and Dave Wiley for support and insights into the Stellwagen Bank ecosystem. The WHOI Marine Mammal Center provided additional funding for this work. Funding support for T.L.S. was provided by the NOAA Dr. Nancy Foster Scholarship. Finally, we thank the 3 anonymous re viewers for their comments and suggestions that improved this manuscript

Development and assessment of a new dermal attachment for short-term tagging studies of baleen whales

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Methods in Ecology and Evolution 6 (2015): 289–297, doi:10.1111/2041-210X.12325.Current studies of fine-scale baleen whale diving and foraging behaviour rely on archival suction cup tags that remain attached over time scales of hours. However, skin irregularities can make suction cup attachment unreliable, and traditional pole deployment of suction cup tags is challenging in moderate sea conditions or when whales are evasive. We developed a new tag attachment to overcome these limitations. The attachment features a short (6·5–7·5 cm) needle that anchors in the whale's dermis (epidermis and blubber) to which a free-floating tag is attached via a severable tethered link. The needle, tag and a detachable ‘carrier rocket’ with fletching are fitted together to form a projectile that can be deployed at distances of up to 20 m using a compressed-air launcher. A corrosive release mechanism allows the tag to separate from the needle after a specified period of time so that the tag can be recovered. The dermal attachment was evaluated during a study of humpback whales (Megaptera novaeangliae) in the Gulf of Maine and then subsequently deployed on bowhead whales (Balaena mysticetus) near Barrow, Alaska. Monitoring of tagged humpback whales indicated that the needle was shed several days after deployment, the attachment site healed shortly thereafter, and there were no discernible behavioural or health effects over time scales of days to months after tagging. Bowhead whales showed little immediate reaction to tagging; the most common response was a prolonged dive right after tag deployment. On average, respiration rates of tagged bowhead whales were elevated after tag attachment, but returned to the same rate as undisturbed bowheads within 1–1·5 h. When compared to suction cups, the dermal anchor provided a more reliable attachment and it can be applied from greater distances and in rougher sea conditions; it is therefore a useful alternative in circumstances where suction cup tags cannot be easily deployed.This study was funded by the U.S. Department of the Interior, Minerals Management Service (MMS; now Bureau of Ocean Energy Management), through Inter-agency Agreement No. M08PG20021 with the U.S. Department of Commerce, National Oceanic and Atmospheric Administration, as part of the MMS Alaska Environmental Studies Program

Fine-scale spatial and temporal acoustic occurrence of island-associated odontocetes near a mid-oceanic atoll in the northern Indian Ocean

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Panicker, D., Baumgartner, M. F., & Stafford, K. M. Fine-scale spatial and temporal acoustic occurrence of island-associated odontocetes near a mid-oceanic atoll in the northern Indian Ocean. Marine Ecology Progress Series, 683, (2022): 195–208, https://doi.org/10.3354/meps13947.Temporal patterns of oceanic predators can provide valuable information on both lunar and diel influences not just on the distributions of these predators, but also on prey patches that are often difficult to study. Mid-oceanic island chains in the northern Indian Ocean have high odontocete occurrence, but the ecology of these animals is not well characterized. We investigated fine-scale spatial and temporal patterns of island-associated odontocetes using passive acoustic monitoring from January 2019 to January 2020 around Kavaratti Island, Lakshadweep, India. Based on opportunistic recordings in the presence of odontocetes, the majority of the detected whistles were likely made by spinner dolphins Stenella longirostris. We identified a resident population whose whistle occurrence was significantly influenced by month, site, and diel and lunar cycles. More acoustic detections were made in the northeast monsoon month of November and fewer during pre-monsoon and southwest monsoon periods. Distinct day-night differences along with fine-scale temporal variability were also observed, suggesting that delphinids use nearshore waters as a daytime resting habitat. Odontocete detections were highest during the new moon period and lowest during the first quarter phase. Detection rates were higher on the south side of the island. Our study shows that solar and lunar cycles modulate odontocete vocal occurrence, presumably through influences on their prey. Similarities of odontocete occurrence around Lakshadweep to other mid-oceanic island chains suggests that an island-associated micronekton community may exist around Lakshadweep that may also be important to other pelagic species targeted by local fisheries.Funding was provided by the Office of Naval Research Marine Mammal Biology Program, USA, under grant N000141812795. We thank Ajith Kumar, the National Centre for Biological Sciences and Idrees Babu for in-country support

Right whale ecology in the northwest Atlantic ocean

The ecology of the North Atlantic right whale (Eubalaena glacialis) was examined at three spatial scales during the summer and early fall on their northern feeding grounds. The diving and foraging behavior of right whales was investigated at spatial scales of hundreds to thousands of meters by tagging right whales with time-depth recorders to document their diving behavior. The vertical distributions of temperature, salinity and copepods were measured along the tagged whale's track with a conductivity-temperature-depth instrument (CTD) and an optical plankton counter (OPC). Right whales were observed diving to and presumably feeding on discrete layers of their primary prey. older stages of the calanoid copepod Calanus finmarchicus, aggregated just above the bottom mixed layer. Simultaneous visual and oceanographic surveys conducted in the lower Bay of Fundy and Roseway Basin were used to examine right whale distribution at spatial scales of tens of kilometers. Right whale occurrence was associated with greater depths and thicker bottom mixed layers in these regions. There was additional evidence of an association between right whales and ocean fronts in Roseway Basin. Right whale distribution was also examined on spatial scales of hundreds of kilometers by outfitting whales with satellite-monitored radio tags. Movements of the tagged whales were compared to climatological and remotely-sensed environmental datasets to elucidate habitat preferences. The tagged whales moved extensively throughout the Gulf of Maine and western Scotian Shelf where they frequented shallow basins with cold bottom waters, but avoided deep, comparatively warmer basins. Two of the right whale ecology studies described here depended on the OPC for measures of right whale prey distribution and abundance. A final study was conducted to investigate the response of the OPC to C. finmarchicus copepodite stage 5 (CS). Comparisons between collocated OPC casts and zooplankton net samples indicated that the OPC was adept at detecting C. finmarchicus C5. A calibration equation was developed to predict C. finmarchicus C5 abundance from OPC-derived particle abundance

Heat shock protein expression during stress and diapause in the marine copepod Calanus finmarchicus

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Insect Physiology 57 (2011): 665-675, doi:10.1016/j.jinsphys.2011.03.007.Calanoid copepods, such as Calanus finmarchicus, are a key component of marine food webs. C. finmarchicus undergoes a facultative diapause during juvenile development, which profoundly affects their seasonal distribution and availability to their predators. The current ignorance of how copepod diapause is regulated limits understanding of copepod population dynamics, distribution, and ecosystem interactions. Heat shock proteins (Hsps) are a superfamily of molecular chaperones characteristically upregulated in response to stress conditions and frequently associated with diapause in other taxa. In this study, 8 heat shock proteins were identified in C. finmarchicus C5 copepodids (Hsp21, Hsp22, p26, Hsp90, and 4 forms of Hsp70), and expression of these transcripts was characterized in response to handling stress and in association with diapause. Hsp21, Hsp22, and Hsp70A (cytosolic subfamily) were induced by handling stress. Expression of Hsp70A was also elevated in shallow active copepodids relative to deep diapausing copepodids, which may reflect induction of this gene by varied stressors in active animals. In contrast, expression of Hsp22 was elevated in deep diapausing animals; Hsp22 may play a role both in short-term stress responses and in protecting proteins from degradation during diapause. Expression of most of the Hsps examined did not vary in response to diapause, perhaps because the diapause of C. finmarchicus is not associated with the extreme environmental conditions (e.g., freezing, desiccation) experienced by many other taxa, such as overwintering insects or Artemia cysts.Funding for AMA was provided by the WHOI Summer Student Fellowship Program and an EPA STAR fellowship

North Atlantic right whale foraging ecology and its role in human-caused mortality

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marine Ecology Progress Series 581 (2017): 165-181, doi:10.3354/meps12315.Endangered North Atlantic right whales Eubalaena glacialis suffer from unacceptably high rates of ship strikes and fishing gear entanglements, but little is known of the role that diving and foraging behavior plays in mediating human-caused mortality. We conducted a study of right whale foraging ecology by attaching tags to whales for short periods of time (hours), tracking their movements during daytime, and repeatedly sampling oceanographic conditions and prey distribution along the whales’ tracks. Right whales were tagged from late winter to late fall in 6 regions of the Gulf of Maine and southwestern Scotian Shelf from 2000 to 2010. The diving behavior of the tagged whales was governed by the vertical distribution of their primary prey, the copepod Calanus finmarchicus. On average, right whales tagged during spring spent 72% of their time in the upper 10 m (within the draft of most large commercial vessels), indicating the need for expanded ship speed restrictions in western Gulf of Maine springtime habitats. One out of every 4 whales dove to within 5 m of the sea floor during the short time they were tagged, spending as much as 45% of their total tagged time in this depth stratum. Right whales dove to the sea floor in each habitat studied except for one (where only 1 whale was tagged). This relatively high incidence of near-bottom diving raises serious concerns about the continued use of floating ground lines in pot and trap gear in coastal Maine and Canadian waters.Support for this research was provided by the NOAA Right Whale Grants Program, Northeast Consortium, Woods Hole Oceanographic Institution, NOAA Northeast Fisheries Science Center, and the Office of Naval Research

Visual predation during springtime foraging of the North Atlantic right whale (Eubalaena glacialis)

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Mammal Science 33 (2017): 991–1013, doi:10.1111/mms.12417.To assess the role that vision plays in the ability of the North Atlantic right whale (Eubalaena glacialis) to detect its primary prey species, the calanoid copepod Calanus finmarchicus, we have compared the absorbance spectrum of the E. glacialis rod visual pigment, the transmittance spectra of C. finmarchicus carotenoid pigments, as well as the downwelling irradiance and horizontal radiance spectra collected during springtime at three locations in the western Gulf of Maine. The E. glacialis rod visual pigment absorbs light maximally at 493 nm, while microspectrophotometric measurements of the C. finmarchicus carotenoid pigments reveal transmission spectra with minima matching very well with the E. glacialis rod visual pigment absorbance spectra maximum. Springtime spectral downwelling irradiance and horizontal radiance values from the surface waters of Cape Cod Bay and at all depths in Great South Channel overlap the E. glacialis rod absorbance spectrum, allowing C. finmarchicus to appear as a high-contrast dark silhouette against a bright background space-light, thus facilitating visually-guided contrast foraging. In contrast, spectral downwelling irradiance and horizontal radiance at depth in Cape Cod Bay, and all depths in Wilkinson Basin, do not overlap the E. glacialis rod absorbance spectrum, providing little if any useful light for contrast vision.This work was supported by Wildlife Bycatch Reduction at the New England Aquarium under U.S. Department of Commerce NOAA Award #NA09NMF4520413 (J.I.F.). T.W.C. was supported by the National Science Foundation (IOS0721608) and the Air Force Office of Scientific Research (FA9550-09-1-0149). Additional support comes from NIH grant 2RO1EY009514 (D.D.Oprian)

Slocum gliders provide accurate near real-time estimates of baleen whale presence from human-reviewed passive acoustic detection information

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baumgartner, M. F., Bonnell, J., Corkeron, P. J., Van Parijs, S. M., Hotchkin, C., Hodges, B. A., Thornton, J. B., Mensi, B. L., & Bruner, S. M. Slocum gliders provide accurate near real-time estimates of baleen whale presence from human-reviewed passive acoustic detection information. Frontiers in Marine Science, 7, (2020):100, doi:10.3389/fmars.2020.00100.Mitigating the effects of human activities on marine mammals often depends on monitoring animal occurrence over long time scales, large spatial scales, and in real time. Passive acoustics, particularly from autonomous vehicles, is a promising approach to meeting this need. We have previously developed the capability to record, detect, classify, and transmit to shore information about the tonal sounds of baleen whales in near real time from long-endurance ocean gliders. We have recently developed a protocol by which a human analyst reviews this information to determine the presence of marine mammals, and the results of this review are automatically posted to a publicly accessible website, sent directly to interested parties via email or text, and made available to stakeholders via a number of public and private digital applications. We evaluated the performance of this system during two 3.75-month Slocum glider deployments in the southwestern Gulf of Maine during the spring seasons of 2015 and 2016. Near real-time detections of humpback, fin, sei, and North Atlantic right whales were compared to detections of these species from simultaneously recorded audio. Data from another 2016 glider deployment in the same area were also used to compare results between three different analysts to determine repeatability of results both among and within analysts. False detection (occurrence) rates on daily time scales were 0% for all species. Daily missed detection rates ranged from 17 to 24%. Agreement between two trained novice analysts and an experienced analyst was greater than 95% for fin, sei, and right whales, while agreement was 83–89% for humpback whales owing to the more subjective process for detecting this species. Our results indicate that the presence of baleen whales can be accurately determined using information about tonal sounds transmitted in near real-time from Slocum gliders. The system is being used operationally to monitor baleen whales in United States, Canadian, and Chilean waters, and has been particularly useful for monitoring the critically endangered North Atlantic right whale throughout the northwestern Atlantic Ocean.Funding for this project was provided by the Environmental Security Technology Certification Program of the U.S. Department of Defense and the U.S. Navy’s Living Marine Resources Program

Pan American Climate Studies (PACS) data report

The surface mooring component of the NOAA Pan American Climate Study (PACS) took place from April 1997 to September 1998 in the eastern tropical Pacific. PACS was a NOAA funded study with the goal of investigating links between sea surface temperature variability in the tropical oceans near the Americas and climate over the American continents. Two air-sea interaction surface moorings were deployed along 125°W, spanning a strong meridional sea-surface temperature gradient. One mooring site was located in the cold tongue south of the equator, and the other site was in the region of warm ocean found north of the equator, near the northernmost summer location of the Intertropical Convergence Zone. The moorings were deployed to improve our understanding of air-sea fluxes and the procsses that control the evolution of the sea surface temperature field in the region. Four air-sea interaction buoys were deployed to occupy two sites for a period of 17 months. The sites were along 125°W near 3°S and 10°N. The Upper Ocean Processes Group at WHOI deployed the first two moorings in April 1997. These moorings were replaced with a second pair of moorings in December 1997. The final recovery occurred in September 1998. Each of these buoys on these moorings were equipped with meteorological instrumentation, including a Vector Averaging Wind Recorder (VAWR) and an Improved METeorological (IMET) system. The moorings also carried Vector Measuring Current Meters (VMCMS), single point temperature recorders and a few conductivity sensors on the mooring line to monitor the upper 200m of the ocean. In addition to the traditional instruments, several other experimental instruments were deployed with limited success on the mooring line including acoustic current meters, acoustic rain gauges and bio-optical instrument packages. This report describes the instrumentation deployed on the PACS surface moorings, along with information on the processing and quality control of the returned data. It presents a detailed overview of the meteorological and physical oceanographic data including time series plots, statistics and spectra of key parameters. It also presents analysis of the estimated air-sea heat, moisture and momentum fluxes.Funding was provided by the National Oceanic and Atmospheric Administration Contract No. NA96GP0428