1
|
Jacobs ER, Gero S, Malinka CE, Tønnesen PH, Beedholm K, DeRuiter SL, Madsen PT. The active space of sperm whale codas: inter-click information for intra-unit communication. J Exp Biol 2024; 227:jeb246442. [PMID: 38264868 DOI: 10.1242/jeb.246442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Sperm whales (Physeter macrocephalus) are social mega-predators who form stable matrilineal units that often associate within a larger vocal clan. Clan membership is defined by sharing a repertoire of coda types consisting of specific temporal spacings of multi-pulsed clicks. It has been hypothesized that codas communicate membership across socially segregated sympatric clans, but others propose that codas are primarily used for behavioral coordination and social cohesion within a closely spaced social unit. Here, we test these hypotheses by combining measures of ambient noise levels and coda click source levels with models of sound propagation to estimate the active space of coda communication. Coda clicks were localized off the island of Dominica with a four- or five-element 80 m vertical hydrophone array, allowing us to calculate the median RMS source levels of 1598 clicks from 444 codas to be 161 dB re. 1 μPa (IQR 153-167), placing codas among the most powerful communication sounds in toothed whales. However, together with measured ambient noise levels, these source levels lead to a median active space of coda communication of ∼4 km, reflecting the maximum footprint of a single foraging sperm whale unit. We conclude that while sperm whale codas may contain information about clan affiliation, their moderate active space shows that codas are not used for long range acoustic communication between units and clans, but likely serve to mediate social cohesion and behavioral transitions in intra-unit communication.
Collapse
Affiliation(s)
- Ellen R Jacobs
- Zoophysiology, Department of Biology, Aarhus University, C. F. Møllers Allé 3, DK-8000 Aarhus C, Denmark
- Department of Biology, Georgetown University, 3700 O St NW, Washington, DC 20057, USA
| | - Shane Gero
- Zoophysiology, Department of Biology, Aarhus University, C. F. Møllers Allé 3, DK-8000 Aarhus C, Denmark
- Department of Biology, Carleton University, 1125 Colonel By Dr, Ottawa, ON, Canada K1S 5B6
| | - Chloe E Malinka
- Zoophysiology, Department of Biology, Aarhus University, C. F. Møllers Allé 3, DK-8000 Aarhus C, Denmark
- SMRU Consulting, Scottish Oceans Institute, East Sands, University of St Andrews, KY16 8LB, UK
| | - Pernille H Tønnesen
- Zoophysiology, Department of Biology, Aarhus University, C. F. Møllers Allé 3, DK-8000 Aarhus C, Denmark
| | - Kristian Beedholm
- Zoophysiology, Department of Biology, Aarhus University, C. F. Møllers Allé 3, DK-8000 Aarhus C, Denmark
| | - Stacy L DeRuiter
- Department of Mathematics and Statistics, Calvin University, 3201 Burton St SE, Grand Rapids, MI 49546, USA
| | - Peter T Madsen
- Zoophysiology, Department of Biology, Aarhus University, C. F. Møllers Allé 3, DK-8000 Aarhus C, Denmark
| |
Collapse
|
2
|
Eddy J, Pham F, Chee R, Park E, Dapprich N, DeRuiter SL, Shen A. Intestinal endothelial cells increase HIV infection and latency in resting and activated CD4 + T cells, particularly affecting CCR6 + CD4 + T cells. Retrovirology 2023; 20:7. [PMID: 37202790 PMCID: PMC10197447 DOI: 10.1186/s12977-023-00621-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/29/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND With suppressive antiretroviral therapy, HIV infection is well-managed in most patients. However, eradication and cure are still beyond reach due to latent viral reservoirs in CD4 + T cells, particularly in lymphoid tissue environments including the gut associated lymphatic tissues. In HIV patients, there is extensive depletion of T helper cells, particularly T helper 17 cells from the intestinal mucosal area, and the gut is one of the largest viral reservoir sites. Endothelial cells line lymphatic and blood vessels and were found to promote HIV infection and latency in previous studies. In this study, we examined endothelial cells specific to the gut mucosal area-intestinal endothelial cells-for their impact on HIV infection and latency in T helper cells. RESULTS We found that intestinal endothelial cells dramatically increased productive and latent HIV infection in resting CD4 + T helper cells. In activated CD4 + T cells, endothelial cells enabled the formation of latent infection in addition to the increase of productive infection. Endothelial-cell-mediated HIV infection was more prominent in memory T cells than naïve T cells, and it involved the cytokine IL-6 but did not involve the co-stimulatory molecule CD2. The CCR6 + T helper 17 subpopulation was particularly susceptible to such endothelial-cell-promoted infection. CONCLUSION Endothelial cells, which are widely present in lymphoid tissues including the intestinal mucosal area and interact regularly with T cells physiologically, significantly increase HIV infection and latent reservoir formation in CD4 + T cells, particularly in CCR6 + T helper 17 cells. Our study highlighted the importance of endothelial cells and the lymphoid tissue environment in HIV pathology and persistence.
Collapse
Affiliation(s)
- Jessica Eddy
- Department of Biology, Calvin University, 3201 Burton St. SE, Grand Rapids, MI 49546 USA
| | - Fisher Pham
- Department of Biology, Calvin University, 3201 Burton St. SE, Grand Rapids, MI 49546 USA
| | - Rachel Chee
- Department of Biology, Calvin University, 3201 Burton St. SE, Grand Rapids, MI 49546 USA
| | - Esther Park
- Department of Biology, Calvin University, 3201 Burton St. SE, Grand Rapids, MI 49546 USA
| | - Nathan Dapprich
- Department of Biology, Calvin University, 3201 Burton St. SE, Grand Rapids, MI 49546 USA
| | - Stacy L. DeRuiter
- Department of Mathematics & Statistics, Calvin University, 3201 Burton St. SE, Grand Rapids, MI 49546 USA
| | - Anding Shen
- Department of Biology, Calvin University, 3201 Burton St. SE, Grand Rapids, MI 49546 USA
| |
Collapse
|
3
|
Goldbogen JA, Cade DE, Wisniewska DM, Potvin J, Segre PS, Savoca MS, Hazen EL, Czapanskiy MF, Kahane-Rapport SR, DeRuiter SL, Gero S, Tønnesen P, Gough WT, Hanson MB, Holt MM, Jensen FH, Simon M, Stimpert AK, Arranz P, Johnston DW, Nowacek DP, Parks SE, Visser F, Friedlaender AS, Tyack PL, Madsen PT, Pyenson ND. Why whales are big but not bigger: Physiological drivers and ecological limits in the age of ocean giants. Science 2020; 366:1367-1372. [PMID: 31831666 DOI: 10.1126/science.aax9044] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/31/2019] [Indexed: 12/27/2022]
Abstract
The largest animals are marine filter feeders, but the underlying mechanism of their large size remains unexplained. We measured feeding performance and prey quality to demonstrate how whale gigantism is driven by the interplay of prey abundance and harvesting mechanisms that increase prey capture rates and energy intake. The foraging efficiency of toothed whales that feed on single prey is constrained by the abundance of large prey, whereas filter-feeding baleen whales seasonally exploit vast swarms of small prey at high efficiencies. Given temporally and spatially aggregated prey, filter feeding provides an evolutionary pathway to extremes in body size that are not available to lineages that must feed on one prey at a time. Maximum size in filter feeders is likely constrained by prey availability across space and time.
Collapse
Affiliation(s)
- J A Goldbogen
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA.
| | - D E Cade
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - D M Wisniewska
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - J Potvin
- Department of Physics, Saint Louis University, St. Louis, MO, USA
| | - P S Segre
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - M S Savoca
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - E L Hazen
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA.,Environmental Research Division, National Oceanic and Atmospheric Administration, Southwest Fisheries Science Center, Monterey, CA, USA.,Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - M F Czapanskiy
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - S R Kahane-Rapport
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - S L DeRuiter
- Mathematics and Statistics Department, Calvin University, Grand Rapids, MI, USA
| | - S Gero
- Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - P Tønnesen
- Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - W T Gough
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - M M Holt
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - F H Jensen
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - M Simon
- Greenland Climate Research Centre, Greenland Institute of Natural Resources, Nuuk, Greenland
| | - A K Stimpert
- Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | - P Arranz
- Biodiversity, Marine Ecology and Conservation Group, Department of Animal Biology, University of La Laguna, La Laguna, Spain
| | - D W Johnston
- Nicholas School of the Environment, Duke University Marine Laboratory, Beaufort, NC, USA
| | - D P Nowacek
- Pratt School of Engineering, Duke University, Durham, NC, USA
| | - S E Parks
- Department of Biology, Syracuse University, Syracuse, NY, USA
| | - F Visser
- Department of Freshwater and Marine Ecology, IBED, University of Amsterdam, Amsterdam, Netherlands.,Department of Coastal Systems, NIOZ and Utrecht University, Utrecht, Netherlands.,Kelp Marine Research, Hoorn, Netherlands
| | - A S Friedlaender
- Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - P L Tyack
- Sea Mammal Research Unit, School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, UK
| | - P T Madsen
- Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.,Aarhus Institute of Advanced Studies, Aarhus University, DK-8000 Aarhus C, Denmark
| | - N D Pyenson
- Department of Paleobiology, National Museum of Natural History, Washington, DC, USA.,Department of Paleontology and Geology, Burke Museum of Natural History and Culture, Seattle, WA, USA
| |
Collapse
|
4
|
Wensveen PJ, Isojunno S, Hansen RR, von Benda-Beckmann AM, Kleivane L, van IJsselmuide S, Lam FPA, Kvadsheim PH, DeRuiter SL, Curé C, Narazaki T, Tyack PL, Miller PJO. Northern bottlenose whales in a pristine environment respond strongly to close and distant navy sonar signals. Proc Biol Sci 2019; 286:20182592. [PMID: 30890101 PMCID: PMC6452067 DOI: 10.1098/rspb.2018.2592] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/25/2019] [Indexed: 11/12/2022] Open
Abstract
Impact assessments for sonar operations typically use received sound levels to predict behavioural disturbance in marine mammals. However, there are indications that cetaceans may learn to associate exposures from distant sound sources with lower perceived risk. To investigate the roles of source distance and received level in an area without frequent sonar activity, we conducted multi-scale controlled exposure experiments ( n = 3) with 12 northern bottlenose whales near Jan Mayen, Norway. Animals were tagged with high-resolution archival tags ( n = 1 per experiment) or medium-resolution satellite tags ( n = 9 in total) and subsequently exposed to sonar. We also deployed bottom-moored recorders to acoustically monitor for whales in the exposed area. Tagged whales initiated avoidance of the sound source over a wide range of distances (0.8-28 km), with responses characteristic of beaked whales. Both onset and intensity of response were better predicted by received sound pressure level (SPL) than by source distance. Avoidance threshold SPLs estimated for each whale ranged from 117-126 dB re 1 µPa, comparable to those of other tagged beaked whales. In this pristine underwater acoustic environment, we found no indication that the source distances tested in our experiments modulated the behavioural effects of sonar, as has been suggested for locations where whales are frequently exposed to sonar.
Collapse
Affiliation(s)
- Paul J. Wensveen
- Sea Mammal Research Unit, School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, UK
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavik, Iceland
| | - Saana Isojunno
- Sea Mammal Research Unit, School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, UK
| | - Rune R. Hansen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Alexander M. von Benda-Beckmann
- Acoustics and Sonar Research Group, Netherlands Organisation for Applied Scientific Research (TNO), The Hague, The Netherlands
| | | | - Sander van IJsselmuide
- Acoustics and Sonar Research Group, Netherlands Organisation for Applied Scientific Research (TNO), The Hague, The Netherlands
| | - Frans-Peter A. Lam
- Acoustics and Sonar Research Group, Netherlands Organisation for Applied Scientific Research (TNO), The Hague, The Netherlands
| | | | - Stacy L. DeRuiter
- Department of Mathematics and Statistics, Calvin College, Grand Rapids, MI, USA
| | - Charlotte Curé
- Cerema—Ifsttar, UMRAE, Laboratoire de Strasbourg, Strasbourg, France
| | - Tomoko Narazaki
- Sea Mammal Research Unit, School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, UK
| | - Peter L. Tyack
- Sea Mammal Research Unit, School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, UK
| | - Patrick J. O. Miller
- Sea Mammal Research Unit, School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, UK
| |
Collapse
|
5
|
Arranz P, Benoit-Bird KJ, Friedlaender AS, Hazen EL, Goldbogen JA, Stimpert AK, DeRuiter SL, Calambokidis J, Southall BL, Fahlman A, Tyack PL. Diving Behavior and Fine-Scale Kinematics of Free-Ranging Risso's Dolphins Foraging in Shallow and Deep-Water Habitats. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
|
6
|
Southall BL, DeRuiter SL, Friedlaender A, Stimpert AK, Goldbogen JA, Hazen E, Casey C, Fregosi S, Cade DE, Allen AN, Harris CM, Schorr G, Moretti D, Guan S, Calambokidis J. Behavioral responses of individual blue whales ( Balaenoptera musculus) to mid-frequency military sonar. ACTA ACUST UNITED AC 2019; 222:222/5/jeb190637. [PMID: 30833464 DOI: 10.1242/jeb.190637] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 01/10/2019] [Indexed: 11/20/2022]
Abstract
This study measured the degree of behavioral responses in blue whales (Balaenoptera musculus) to controlled noise exposure off the southern California coast. High-resolution movement and passive acoustic data were obtained from non-invasive archival tags (n=42) whereas surface positions were obtained with visual focal follows. Controlled exposure experiments (CEEs) were used to obtain direct behavioral measurements before, during and after simulated and operational military mid-frequency active sonar (MFAS), pseudorandom noise (PRN) and controls (no noise exposure). For a subset of deep-feeding animals (n=21), active acoustic measurements of prey were obtained and used as contextual covariates in response analyses. To investigate potential behavioral changes within individuals as a function of controlled noise exposure conditions, two parallel analyses of time-series data for selected behavioral parameters (e.g. diving, horizontal movement and feeding) were conducted. This included expert scoring of responses according to a specified behavioral severity rating paradigm and quantitative change-point analyses using Mahalanobis distance statistics. Both methods identified clear changes in some conditions. More than 50% of blue whales in deep-feeding states responded during CEEs, whereas no changes in behavior were identified in shallow-feeding blue whales. Overall, responses were generally brief, of low to moderate severity, and highly dependent on exposure context such as behavioral state, source-to-whale horizontal range and prey availability. Response probability did not follow a simple exposure-response model based on received exposure level. These results, in combination with additional analytical methods to investigate different aspects of potential responses within and among individuals, provide a comprehensive evaluation of how free-ranging blue whales responded to mid-frequency military sonar.
Collapse
Affiliation(s)
- Brandon L Southall
- Southall Environmental Associates (SEA), Inc., Aptos, CA 95003, USA .,Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Stacy L DeRuiter
- Department of Mathematics and Statistics, Calvin College, Grand Rapids, MI 49546, USA
| | - Ari Friedlaender
- Southall Environmental Associates (SEA), Inc., Aptos, CA 95003, USA.,Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
| | - Alison K Stimpert
- Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA 95039, USA
| | - Jeremy A Goldbogen
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Elliott Hazen
- Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,NOAA Southwest Fisheries Science Center, Monterey, CA 93940, USA
| | - Caroline Casey
- Southall Environmental Associates (SEA), Inc., Aptos, CA 95003, USA.,Institute of Marine Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Selene Fregosi
- Southall Environmental Associates (SEA), Inc., Aptos, CA 95003, USA.,Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
| | - David E Cade
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - Ann N Allen
- Cascadia Research Collective, Olympia, WA 98501, USA
| | - Catriona M Harris
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews KY16 9LZ, UK
| | - Greg Schorr
- Marine Ecology and Telemetry Research, Seabeck, WA 98380, USA
| | - David Moretti
- Naval Undersea Warfare Center, Newport, RI 02841, USA
| | - Shane Guan
- Office of Protected Resources, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Silver Spring, MD 20910, USA
| | | |
Collapse
|
7
|
Visser F, Kok AC, Oudejans MG, Scott-Hayward LA, DeRuiter SL, Alves AC, Antunes RN, Isojunno S, Pierce GJ, Slabbekoorn H, Huisman J, Miller PJO. Vocal foragers and silent crowds: context-dependent vocal variation in Northeast Atlantic long-finned pilot whales. Behav Ecol Sociobiol 2017; 71:170. [PMID: 29167596 PMCID: PMC5674111 DOI: 10.1007/s00265-017-2397-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 11/12/2022]
Abstract
ABSTRACT Vocalisations form a key component of the social interactions and foraging behaviour of toothed whales. We investigated changes in calling and echolocation behaviour of long-finned pilot whales between foraging and non-foraging periods, by combining acoustic recordings and diving depth data from tagged individuals with concurrent surface observations on social behaviour of their group. The pilot whales showed marked vocal variation, specific to foraging and social context. During periods of foraging, pilot whales showed more vocal activity than during non-foraging periods (rest, travel). In addition to the expected increase in echolocation activity, call rates also increased, suggesting that pilot whales communicate more during foraging. Furthermore, calls with multiple inflections occurred more often immediately before and after foraging dives and during the early descent and late ascent phases of foraging dives. However, these calls were almost never detected at diving depths of the tagged whale beyond 350 m. Calls with no or few inflections were produced at all times, irrespective of diving depth of the tagged whale. We discuss possible explanations for the distinct vocal variation associated with foraging periods. In addition, during non-foraging periods, the pilot whales were found to be more silent (no calling or echolocation) in larger, more closely spaced groups. This indicates that increased levels of social cohesion may release the need to stay in touch acoustically. SIGNIFICANCE STATEMENT Social toothed whales rely on vocalisations to find prey and interact with conspecifics. Species are often highly vocal and can have elaborate call repertoires. However, it often remains unclear how their repertoire use correlates to specific social and behavioural contexts, which is vital to understand toothed whale foraging strategies and sociality. Combining on-animal tag recordings of diving and acoustic behaviour with observations of social behaviour, we found that pilot whales produce more calls during foraging than during non-foraging periods. Moreover, highly inflected calls were closely associated to the periods around and during foraging dives. This indicates enhanced communication during foraging, which may, for example, enable relocation of conspecifics or sharing of information. Whales reduced their vocal activity (calling and echolocation) at increased levels of social cohesion, indicating that in certain behavioural contexts, closer association (i.e. more closely spaced) may release the need to stay in touch acoustically.
Collapse
Affiliation(s)
- Fleur Visser
- Behavioural Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Kelp Marine Research, Hoorn, The Netherlands
| | - Annebelle C.M. Kok
- Behavioural Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Lindesay A.S. Scott-Hayward
- Centre for Research into Ecological and Environmental Modelling (CREEM), University of St Andrews, Scotland, UK
| | - Stacy L. DeRuiter
- Centre for Research into Ecological and Environmental Modelling (CREEM), University of St Andrews, Scotland, UK
- Department of Mathematics and Statistics, Calvin College, Grand Rapids, MI USA
| | - Ana C. Alves
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Scotland, UK
| | - Ricardo N. Antunes
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Scotland, UK
- Ocean Giants Program, Wildlife Conservation Society, New York, NY USA
| | - Saana Isojunno
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Scotland, UK
| | - Graham J. Pierce
- Oceanlab, University of Aberdeen, Aberdeenshire, UK
- CESAM and Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
- CSIC, Vigo, Spain
| | - Hans Slabbekoorn
- Behavioural Biology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Jef Huisman
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Patrick J. O. Miller
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Scotland, UK
| |
Collapse
|
8
|
Falcone EA, Schorr GS, Watwood SL, DeRuiter SL, Zerbini AN, Andrews RD, Morrissey RP, Moretti DJ. Diving behaviour of Cuvier's beaked whales exposed to two types of military sonar. R Soc Open Sci 2017; 4:170629. [PMID: 28879004 PMCID: PMC5579120 DOI: 10.1098/rsos.170629] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/02/2017] [Indexed: 05/17/2023]
Abstract
Cuvier's beaked whales (Ziphius cavirostris) have stranded in association with mid-frequency active sonar (MFAS) use, and though the causative mechanism linking these events remains unclear, it is believed to be behaviourally mediated. To determine whether MFAS use was associated with behavioural changes in this species, satellite tags were used to record the diving and movements of 16 Cuvier's beaked whales for up to 88 days in a region of frequent MFAS training off the coast of Southern California. Tag data were combined with summarized records of concurrent bouts of high-power, surface-ship and mid-power, helicopter-deployed MFAS use, along with other potential covariates, in generalized additive mixed-effects models. Deep dives, shallow dives and surface intervals tended to become longer during MFAS use, with some variation associated with the total amount of overlapping MFAS during the behaviour. These changes in dives and surface intervals contributed to a longer interval between deep dives, a proxy for foraging disruption in this species. Most responses intensified with proximity and were more pronounced during mid-power than high-power MFAS use at comparable distances within approximately 50 km, despite the significantly lower source level of mid-power MFAS. However, distance-mediated responses to high-power MFAS, and increased deep dive intervals during mid-power MFAS, were evident up to approximately 100 km away.
Collapse
Affiliation(s)
- Erin A. Falcone
- Marine Ecology and Telemetry Research, 2420 Nellita Rd NW, Seabeck, WA 98380, USA
- Author for correspondence: Erin A. Falcone e-mail:
| | - Gregory S. Schorr
- Marine Ecology and Telemetry Research, 2420 Nellita Rd NW, Seabeck, WA 98380, USA
| | | | - Stacy L. DeRuiter
- Department of Mathematics and Statistics, Calvin College, 1740 Knollcrest Circle SE, Grand Rapids, MI 49546, USA
| | - Alexandre N. Zerbini
- Marine Ecology and Telemetry Research, 2420 Nellita Rd NW, Seabeck, WA 98380, USA
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NMFS-NOAA, 7600 Sand Point Way NE, Seattle, WA 98115, USA
- Cascadia Research Collective, 218 ½ W 4th Avenue, Olympia, WA 98501, USA
| | - Russel D. Andrews
- Marine Ecology and Telemetry Research, 2420 Nellita Rd NW, Seabeck, WA 98380, USA
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, PO Box 757220, Fairbanks, AK 99775, USA
| | | | - David J. Moretti
- Naval Undersea Warfare Center Division, Code 74, Newport, RI 02840, USA
| |
Collapse
|
9
|
Falcone EA, Schorr GS, Watwood SL, DeRuiter SL, Zerbini AN, Andrews RD, Morrissey RP, Moretti DJ. Diving behaviour of Cuvier's beaked whales exposed to two types of military sonar. R Soc Open Sci 2017. [PMID: 28879004 DOI: 10.5061/dryad.125g5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cuvier's beaked whales (Ziphius cavirostris) have stranded in association with mid-frequency active sonar (MFAS) use, and though the causative mechanism linking these events remains unclear, it is believed to be behaviourally mediated. To determine whether MFAS use was associated with behavioural changes in this species, satellite tags were used to record the diving and movements of 16 Cuvier's beaked whales for up to 88 days in a region of frequent MFAS training off the coast of Southern California. Tag data were combined with summarized records of concurrent bouts of high-power, surface-ship and mid-power, helicopter-deployed MFAS use, along with other potential covariates, in generalized additive mixed-effects models. Deep dives, shallow dives and surface intervals tended to become longer during MFAS use, with some variation associated with the total amount of overlapping MFAS during the behaviour. These changes in dives and surface intervals contributed to a longer interval between deep dives, a proxy for foraging disruption in this species. Most responses intensified with proximity and were more pronounced during mid-power than high-power MFAS use at comparable distances within approximately 50 km, despite the significantly lower source level of mid-power MFAS. However, distance-mediated responses to high-power MFAS, and increased deep dive intervals during mid-power MFAS, were evident up to approximately 100 km away.
Collapse
Affiliation(s)
- Erin A Falcone
- Marine Ecology and Telemetry Research, 2420 Nellita Rd NW, Seabeck, WA 98380, USA
| | - Gregory S Schorr
- Marine Ecology and Telemetry Research, 2420 Nellita Rd NW, Seabeck, WA 98380, USA
| | | | - Stacy L DeRuiter
- Department of Mathematics and Statistics, Calvin College, 1740 Knollcrest Circle SE, Grand Rapids, MI 49546, USA
| | - Alexandre N Zerbini
- Marine Ecology and Telemetry Research, 2420 Nellita Rd NW, Seabeck, WA 98380, USA
- Marine Mammal Laboratory, Alaska Fisheries Science Center, NMFS-NOAA, 7600 Sand Point Way NE, Seattle, WA 98115, USA
- Cascadia Research Collective, 218 ½ W 4th Avenue, Olympia, WA 98501, USA
| | - Russel D Andrews
- Marine Ecology and Telemetry Research, 2420 Nellita Rd NW, Seabeck, WA 98380, USA
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, PO Box 757220, Fairbanks, AK 99775, USA
| | | | - David J Moretti
- Naval Undersea Warfare Center Division, Code 74, Newport, RI 02840, USA
| |
Collapse
|
10
|
DeRuiter SL, Langrock R, Skirbutas T, Goldbogen JA, Calambokidis J, Friedlaender AS, Southall BL. A multivariate mixed hidden Markov model for blue whale behaviour and responses to sound exposure. Ann Appl Stat 2017. [DOI: 10.1214/16-aoas1008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
11
|
Popov V, Langrock R, DeRuiter SL, Visser F. An analysis of pilot whale vocalization activity using hidden Markov models. J Acoust Soc Am 2017; 141:159. [PMID: 28147612 DOI: 10.1121/1.4973624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Vocalizations of cetaceans form a key component of their social interactions. Such vocalization activity is driven by the behavioral states of the whales, which are not directly observable, so that latent-state models are natural candidates for modeling empirical data on vocalizations. In this paper, hidden Markov models are used to analyze calling activity of long-finned pilot whales (Globicephala melas) recorded over three years in the Vestfjord basin off Lofoten, Norway. Baseline models are used to motivate the use of three states, while more complex models are fit to study the influence of covariates on the state-switching dynamics. The analysis demonstrates the potential usefulness of hidden Markov models to concisely yet accurately describe the stochastic patterns found in animal communication data, thereby providing a framework for drawing meaningful biological inference.
Collapse
Affiliation(s)
- Valentin Popov
- School of Mathematics and Statistics, University of St. Andrews, The Observatory, Buchanan Gardens, St. Andrews, KY16 9LZ, United Kingdom
| | - Roland Langrock
- Department of Business Administration and Economics, Bielefeld University, Postfach 10 01 31, 33501 Bielefeld, Germany
| | - Stacy L DeRuiter
- Mathematics and Statistics Department, Calvin College, 3201 Burton Southeast, Grand Rapids, Michigan 49546, USA
| | - Fleur Visser
- Kelp Marine Research, Loniusstraat 9, 1624 CJ, Hoorn, the Netherlands
| |
Collapse
|
12
|
Arranz P, DeRuiter SL, Stimpert AK, Neves S, Friedlaender AS, Goldbogen JA, Visser F, Calambokidis J, Southall BL, Tyack PL. Discrimination of fast click-series produced by tagged Risso's dolphins (Grampus griseus) for echolocation or communication. ACTA ACUST UNITED AC 2016; 219:2898-2907. [PMID: 27401759 DOI: 10.1242/jeb.144295] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/05/2016] [Indexed: 11/20/2022]
Abstract
Early studies that categorized odontocete pulsed sounds had few means of discriminating signals used for biosonar-based foraging from those used for communication. This capability to identify the function of sounds is important for understanding and interpreting behavior; it is also essential for monitoring and mitigating potential disturbance from human activities. Archival tags were placed on free-ranging Grampus griseus to quantify and discriminate between pulsed sounds used for echolocation-based foraging and those used for communication. Two types of rapid click-series pulsed sounds, buzzes and burst pulses, were identified as produced by the tagged dolphins and classified using a Gaussian mixture model based on their duration, association with jerk (i.e. rapid change of acceleration) and temporal association with click trains. Buzzes followed regular echolocation clicks and coincided with a strong jerk signal from accelerometers on the tag. They consisted of series averaging 359±210 clicks (mean±s.d.) with an increasing repetition rate and relatively low amplitude. Burst pulses consisted of relatively short click series averaging 45±54 clicks with decreasing repetition rate and longer inter-click interval that were less likely to be associated with regular echolocation and the jerk signal. These results suggest that the longer, relatively lower amplitude, jerk-associated buzzes are used in this species to capture prey, mostly during the bottom phase of foraging dives, as seen in other odontocetes. In contrast, the shorter, isolated burst pulses that are generally emitted by the dolphins while at or near the surface are used outside of a direct, known foraging context.
Collapse
Affiliation(s)
- P Arranz
- Sea Mammal Research Unit, School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
| | - S L DeRuiter
- Centre for Research into Ecological and Environmental Modelling, School of Mathematics and Statistics, University of St Andrews, St Andrews KY16 9LZ, UK Department of Mathematics and Statistics, Calvin College, Grand Rapids, MI 49546, USA
| | - A K Stimpert
- Vertebrate Ecology Lab, Moss Landing Marine Laboratories, Moss Landing, CA 95039, USA
| | - S Neves
- Sea Mammal Research Unit, School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
| | - A S Friedlaender
- Department of Fisheries and Wildlife, Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR 97635, USA
| | - J A Goldbogen
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
| | - F Visser
- Kelp Marine Research, Hoorn 1624 CJ, The Netherlands Institute of Biology, Leiden University, Leiden 2311, The Netherlands
| | | | - B L Southall
- Southall Environmental Associates, Aptos, CA 95003, USA University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - P L Tyack
- Sea Mammal Research Unit, School of Biology, University of St Andrews, St Andrews KY16 8LB, UK
| |
Collapse
|
13
|
Kershenbaum A, Blumstein DT, Roch MA, Akçay Ç, Backus G, Bee MA, Bohn K, Cao Y, Carter G, Cäsar C, Coen M, DeRuiter SL, Doyle L, Edelman S, Ferrer-i-Cancho R, Freeberg TM, Garland EC, Gustison M, Harley HE, Huetz C, Hughes M, Bruno JH, Ilany A, Jin DZ, Johnson M, Ju C, Karnowski J, Lohr B, Manser MB, McCowan B, Mercado E, Narins PM, Piel A, Rice M, Salmi R, Sasahara K, Sayigh L, Shiu Y, Taylor C, Vallejo EE, Waller S, Zamora-Gutierrez V. Acoustic sequences in non-human animals: a tutorial review and prospectus. Biol Rev Camb Philos Soc 2016; 91:13-52. [PMID: 25428267 PMCID: PMC4444413 DOI: 10.1111/brv.12160] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 10/02/2014] [Accepted: 10/15/2014] [Indexed: 11/30/2022]
Abstract
Animal acoustic communication often takes the form of complex sequences, made up of multiple distinct acoustic units. Apart from the well-known example of birdsong, other animals such as insects, amphibians, and mammals (including bats, rodents, primates, and cetaceans) also generate complex acoustic sequences. Occasionally, such as with birdsong, the adaptive role of these sequences seems clear (e.g. mate attraction and territorial defence). More often however, researchers have only begun to characterise - let alone understand - the significance and meaning of acoustic sequences. Hypotheses abound, but there is little agreement as to how sequences should be defined and analysed. Our review aims to outline suitable methods for testing these hypotheses, and to describe the major limitations to our current and near-future knowledge on questions of acoustic sequences. This review and prospectus is the result of a collaborative effort between 43 scientists from the fields of animal behaviour, ecology and evolution, signal processing, machine learning, quantitative linguistics, and information theory, who gathered for a 2013 workshop entitled, 'Analysing vocal sequences in animals'. Our goal is to present not just a review of the state of the art, but to propose a methodological framework that summarises what we suggest are the best practices for research in this field, across taxa and across disciplines. We also provide a tutorial-style introduction to some of the most promising algorithmic approaches for analysing sequences. We divide our review into three sections: identifying the distinct units of an acoustic sequence, describing the different ways that information can be contained within a sequence, and analysing the structure of that sequence. Each of these sections is further subdivided to address the key questions and approaches in that area. We propose a uniform, systematic, and comprehensive approach to studying sequences, with the goal of clarifying research terms used in different fields, and facilitating collaboration and comparative studies. Allowing greater interdisciplinary collaboration will facilitate the investigation of many important questions in the evolution of communication and sociality.
Collapse
Affiliation(s)
- Arik Kershenbaum
- National Institute for Mathematical and Biological Synthesis, 1122 Volunteer Blvd., Suite 106, University of Tennessee, Knoxville, TN 37996-3410, USA
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Marie A. Roch
- Department of Computer Science, San Diego State University, 5500 Campanile Dr, San Diego, CA 92182, USA
| | - Çağlar Akçay
- Lab of Ornithology, Cornell University, 159 Sapsucker Woods Rd, Ithaca, NY 14850, USA
| | - Gregory Backus
- Department of Biomathematics, North Carolina State University, Raleigh, NC 27607, USA
| | - Mark A. Bee
- Department of Ecology, Evolution and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Cir, Falcon Heights, MN 55108, USA
| | - Kirsten Bohn
- Integrated Science, Florida International University, Modesto Maidique Campus, 11200 SW 8th Street, AHC-4, 351, Miami, FL 33199, USA
| | - Yan Cao
- Department of Mathematical Sciences, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA
| | - Gerald Carter
- Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Cristiane Cäsar
- Department of Psychology & Neuroscience, University of St. Andrews, St Mary’s Quad South Street, St Andrews, Fife, KY16 9JP, UK
| | - Michael Coen
- Department of Biostatistics and Medical Informatics, University of Wisconsin, K6/446 Clinical Sciences Center, 600 Highland Avenue, Madison, WI 53792-4675, USA
| | - Stacy L. DeRuiter
- School of Mathematics and Statistics, University of St. Andrews, St Andrews, KY16 9SS, UK
| | - Laurance Doyle
- Carl Sagan Center for the Study of Life in the Universe, SETI Institute, 189 Bernardo Ave, Suite 100, Mountain View, CA 94043, USA
| | - Shimon Edelman
- Department of Psychology, Cornell University, 211 Uris Hall, Ithaca, NY 14853-7601, USA
| | - Ramon Ferrer-i-Cancho
- Department of Computer Science, Universitat Politecnica de Catalunya, (Catalonia), Calle Jordi Girona, 31, 08034 Barcelona, Spain
| | - Todd M. Freeberg
- Department of Psychology, University of Tennessee, Austin Peay Building, Knoxville, Tennessee 37996, USA
| | - Ellen C. Garland
- National Marine Mammal Laboratory, AFSC/NOAA, 7600 Sand Point Way N.E., Seattle, Washington 98115, USA
| | - Morgan Gustison
- Department of Psychology, University of Michigan, 530 Church St, Ann Arbor, MI 48109, USA
| | - Heidi E. Harley
- Division of Social Sciences, New College of Florida, 5800 Bay Shore Rd, Sarasota, FL 34243, USA
| | - Chloé Huetz
- CNPS, CNRS UMR 8195, Université Paris-Sud, UMR 8195, Batiments 440-447, Rue Claude Bernard, 91405 Orsay, France
| | - Melissa Hughes
- Department of Biology, College of Charleston, 66 George St, Charleston, SC 29424, USA
| | - Julia Hyland Bruno
- Department of Psychology, Hunter College and the Graduate Center, The City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Amiyaal Ilany
- National Institute for Mathematical and Biological Synthesis, 1122 Volunteer Blvd., Suite 106, University of Tennessee, Knoxville, TN 37996-3410, USA
| | - Dezhe Z. Jin
- Department of Physics, Pennsylvania State University, 104 Davey Lab, University Park, PA 16802-6300, USA
| | - Michael Johnson
- Department of Electrical and Computer Engineering, Marquette University, 1515 W. Wisconsin Ave., Milwaukee, WI 53233, USA
| | - Chenghui Ju
- Department of Biology, Queen College, The City Univ. of New York, 65-30 Kissena Blvd., Flushing, New York 11367, USA
| | - Jeremy Karnowski
- Department of Cognitive Science, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0515, USA
| | - Bernard Lohr
- Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Marta B. Manser
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Brenda McCowan
- Department of Veterinary Medicine, University of California Davis, 1 Peter J Shields Ave, Davis, CA 95616, USA
| | - Eduardo Mercado
- Department of Psychology; Evolution, Ecology, & Behavior, University at Buffalo, The State University of New York, Park Hall Room 204, Buffalo, NY 14260-4110, USA
| | - Peter M. Narins
- Department of Integrative Biology & Physiology, University of California Los Angeles, 612 Charles E. Young Drive East, Los Angeles, CA 90095-7246, USA
| | - Alex Piel
- Division of Biological Anthropology, University of Cambridge, Pembroke Street Cambridge, CB2 3QG, UK
| | - Megan Rice
- Department of Psychology, California State University San Marcos, 333 S. Twin Oaks Valley Rd., San Marcos, CA 92096-0001, USA
| | - Roberta Salmi
- Department of Anthropology, University of Georgia at Athens, 355 S Jackson St, Athens, GA 30602, USA
| | - Kazutoshi Sasahara
- Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Laela Sayigh
- Biology Department, Woods Hole Oceanographic Institution, 86 Water St, Woods Hole, MA 02543, USA
| | - Yu Shiu
- Lab of Ornithology, Cornell University, 159 Sapsucker Woods Rd, Ithaca, NY 14850, USA
| | - Charles Taylor
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, 621 Charles E. Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Edgar E. Vallejo
- Department of Computer Science, Monterrey Institute of Technology, Ave. Eugenio Garza Sada 2501 Sur Col. Tecnológico C.P. 64849, Monterrey, Nuevo León, Mexico
| | - Sara Waller
- Department of Philosophy, Montana State University, 2-155 Wilson Hall, Bozeman, Montana 59717, USA
| | - Veronica Zamora-Gutierrez
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
- Centre for Biodiversity and Environmental Research, University College London, London WC1H 0AG, UK
| |
Collapse
|
14
|
Goldbogen JA, Hazen EL, Friedlaender AS, Calambokidis J, DeRuiter SL, Stimpert AK, Southall BL. Prey density and distribution drive the three‐dimensional foraging strategies of the largest filter feeder. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12395] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jeremy A. Goldbogen
- Department of Biology Hopkins Marine Station Stanford University Pacific Grove California 93950 USA
| | - Elliott L. Hazen
- NOAA/NMFS/SWFSC/Environmental Research Division Pacific Grove California 93950 USA
| | - Ari S. Friedlaender
- Marine Mammal Institute Hatfield Marine Science Center Oregon State University Newport Oregon 97365 USA
| | - John Calambokidis
- Cascadia Research Collective 218 1/2 W. 4th AvenueOlympia Washington 98501 USA
| | | | - Alison K. Stimpert
- Moss Landing Marine Laboratories 8272 Moss Landing RoadMoss Landing California 95039 USA
| | - Brandon L. Southall
- Southall Environmental Associates Inc. 9099 Soquel Drive, Suite 8 Aptos California 95003 USA
- Long Marine Laboratory University of California Institute of Marine Sciences 100 Shaffer Road Santa Cruz California 95060 USA
| |
Collapse
|
15
|
Langrock R, Kneib T, Sohn A, DeRuiter SL. Nonparametric inference in hidden Markov models using P-splines. Biometrics 2015; 71:520-8. [PMID: 25586063 DOI: 10.1111/biom.12282] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 11/01/2014] [Accepted: 11/01/2014] [Indexed: 11/28/2022]
Abstract
Hidden Markov models (HMMs) are flexible time series models in which the distribution of the observations depends on unobserved serially correlated states. The state-dependent distributions in HMMs are usually taken from some class of parametrically specified distributions. The choice of this class can be difficult, and an unfortunate choice can have serious consequences for example on state estimates, and more generally on the resulting model complexity and interpretation. We demonstrate these practical issues in a real data application concerned with vertical speeds of a diving beaked whale, where we demonstrate that parametric approaches can easily lead to overly complex state processes, impeding meaningful biological inference. In contrast, for the dive data, HMMs with nonparametrically estimated state-dependent distributions are much more parsimonious in terms of the number of states and easier to interpret, while fitting the data equally well. Our nonparametric estimation approach is based on the idea of representing the densities of the state-dependent distributions as linear combinations of a large number of standardized B-spline basis functions, imposing a penalty term on non-smoothness in order to maintain a good balance between goodness-of-fit and smoothness.
Collapse
Affiliation(s)
| | | | | | - Stacy L DeRuiter
- University of St Andrews, St Andrews, UK.,Calvin College, Grand Rapids, Michigan, U.S.A
| |
Collapse
|
16
|
Stimpert AK, DeRuiter SL, Southall BL, Moretti DJ, Falcone EA, Goldbogen JA, Friedlaender A, Schorr GS, Calambokidis J. Acoustic and foraging behavior of a Baird's beaked whale, Berardius bairdii, exposed to simulated sonar. Sci Rep 2014; 4:7031. [PMID: 25391309 PMCID: PMC4229675 DOI: 10.1038/srep07031] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/21/2014] [Indexed: 11/09/2022] Open
Abstract
Beaked whales are hypothesized to be particularly sensitive to anthropogenic noise, based on previous strandings and limited experimental and observational data. However, few species have been studied in detail. We describe the underwater behavior of a Baird's beaked whale (Berardius bairdii) from the first deployment of a multi-sensor acoustic tag on this species. The animal exhibited shallow (23 ± 15 m max depth), intermediate (324 ± 49 m), and deep (1138 ± 243 m) dives. Echolocation clicks were produced with a mean inter-click interval of approximately 300 ms and peak frequency of 25 kHz. Two deep dives included presumed foraging behavior, with echolocation pulsed sounds (presumed prey capture attempts) associated with increased maneuvering, and sustained inverted swimming during the bottom phase of the dive. A controlled exposure to simulated mid-frequency active sonar (3.5-4 kHz) was conducted 4 hours after tag deployment, and within 3 minutes of exposure onset, the tagged whale increased swim speed and body movement, and continued to show unusual dive behavior for each of its next three dives, one of each type. These are the first data on the acoustic foraging behavior in this largest beaked whale species, and the first experimental demonstration of a response to simulated sonar.
Collapse
Affiliation(s)
- A K Stimpert
- 1] Department of Oceanography, Naval Postgraduate School, Monterey, CA [2] Vertebrate Ecology Lab, Moss Landing Marine Laboratories, Moss Landing, CA
| | - S L DeRuiter
- Centre for Research into Ecological and Environmental Modeling, University of St. Andrews, St. Andrews, UK
| | - B L Southall
- Southall Environmental Associates, Inc., Aptos, CA
| | | | | | - J A Goldbogen
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA
| | - A Friedlaender
- Sea and Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR
| | - G S Schorr
- Cascadia Research Collective, Olympia, WA
| | | |
Collapse
|
17
|
Goldbogen JA, Stimpert AK, DeRuiter SL, Calambokidis J, Friedlaender AS, Schorr GS, Moretti DJ, Tyack PL, Southall BL. Using accelerometers to determine the calling behavior of tagged baleen whales. J Exp Biol 2014; 217:2449-55. [DOI: 10.1242/jeb.103259] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Low-frequency acoustic signals generated by baleen whales can propagate over vast distances, making the assignment of calls to specific individuals problematic. Here we report the novel use of acoustic recording tags equipped with high-resolution accelerometers to detect vibrations on the surface of two tagged fin whales that directly match the timing of recorded acoustic signals. A tag deployed on a buoy in the vicinity of calling fin whales, and a recording from a tag that had just fallen off of a whale, were able to detect calls acoustically but did not record corresponding accelerometer signals that were measured on calling individuals. Across the hundreds of calls measured on two tagged fin whales, the accelerometer response was generally anisotropic across all three axes, appeared to depend on tag placement, and increased with the level of received sound. These data demonstrate that high-sample-rate accelerometry can provide important insights into the acoustic behavior of baleen whales that communicate at low frequencies. This method helps identify vocalizing whales, which in turn enables the quantification of call rates, a fundamental component of models used to estimate baleen whale abundance and distribution from passive acoustic monitoring.
Collapse
|
18
|
Goldbogen JA, Southall BL, DeRuiter SL, Calambokidis J, Friedlaender AS, Hazen EL, Falcone EA, Schorr GS, Douglas A, Moretti DJ, Kyburg C, McKenna MF, Tyack PL. Blue whales respond to simulated mid-frequency military sonar. Proc Biol Sci 2013; 280:20130657. [PMID: 23825206 PMCID: PMC3712439 DOI: 10.1098/rspb.2013.0657] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Mid-frequency military (1–10 kHz) sonars have been associated with lethal mass strandings of deep-diving toothed whales, but the effects on endangered baleen whale species are virtually unknown. Here, we used controlled exposure experiments with simulated military sonar and other mid-frequency sounds to measure behavioural responses of tagged blue whales (Balaenoptera musculus) in feeding areas within the Southern California Bight. Despite using source levels orders of magnitude below some operational military systems, our results demonstrate that mid-frequency sound can significantly affect blue whale behaviour, especially during deep feeding modes. When a response occurred, behavioural changes varied widely from cessation of deep feeding to increased swimming speed and directed travel away from the sound source. The variability of these behavioural responses was largely influenced by a complex interaction of behavioural state, the type of mid-frequency sound and received sound level. Sonar-induced disruption of feeding and displacement from high-quality prey patches could have significant and previously undocumented impacts on baleen whale foraging ecology, individual fitness and population health.
Collapse
Affiliation(s)
- Jeremy A Goldbogen
- Cascadia Research Collective, 218 1/2 W. 4th Avenue, Olympia, WA 98501, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
DeRuiter SL, Southall BL, Calambokidis J, Zimmer WMX, Sadykova D, Falcone EA, Friedlaender AS, Joseph JE, Moretti D, Schorr GS, Thomas L, Tyack PL. First direct measurements of behavioural responses by Cuvier's beaked whales to mid-frequency active sonar. Biol Lett 2013; 9:20130223. [PMID: 23825085 PMCID: PMC3730631 DOI: 10.1098/rsbl.2013.0223] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Most marine mammal strandings coincident with naval sonar exercises have involved Cuvier's beaked whales (Ziphius cavirostris). We recorded animal movement and acoustic data on two tagged Ziphius and obtained the first direct measurements of behavioural responses of this species to mid-frequency active (MFA) sonar signals. Each recording included a 30-min playback (one 1.6-s simulated MFA sonar signal repeated every 25 s); one whale was also incidentally exposed to MFA sonar from distant naval exercises. Whales responded strongly to playbacks at low received levels (RLs; 89–127 dB re 1 µPa): after ceasing normal fluking and echolocation, they swam rapidly, silently away, extending both dive duration and subsequent non-foraging interval. Distant sonar exercises (78–106 dB re 1 µPa) did not elicit such responses, suggesting that context may moderate reactions. The observed responses to playback occurred at RLs well below current regulatory thresholds; equivalent responses to operational sonars could elevate stranding risk and reduce foraging efficiency.
Collapse
Affiliation(s)
- Stacy L DeRuiter
- Centre for Research into Ecological and Environmental Modelling, Scottish Oceans Institute, University of St Andrews, , St Andrews, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Goldbogen JA, Calambokidis J, Friedlaender AS, Francis J, DeRuiter SL, Stimpert AK, Falcone E, Southall BL. Underwater acrobatics by the world's largest predator: 360° rolling manoeuvres by lunge-feeding blue whales. Biol Lett 2013. [PMID: 23193050 DOI: 10.1098/rsbl.2012.0986] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The extreme body size of blue whales requires a high energy intake and therefore demands efficient foraging strategies. As an obligate lunge feeder on aggregations of small zooplankton, blue whales engulf a large volume of prey-laden water in a single, rapid gulp. The efficiency of this feeding mechanism is strongly dependent on the amount of prey that can be captured during each lunge, yet food resources tend to be patchily distributed in both space and time. Here, we measured the three-dimensional kinematics and foraging behaviour of blue whales feeding on krill, using suction-cup attached multi-sensor tags. Our analyses revealed 360° rolling lunge-feeding manoeuvres that reorient the body and position the lower jaws so that a krill patch can be engulfed with the whale's body inverted. We also recorded these rolling behaviours when whales were in a searching mode in between lunges, suggesting that this behaviour also enables the whale to visually process the prey field and maximize foraging efficiency by surveying for the densest prey aggregations. These results reveal the complex manoeuvrability that is required for large rorqual whales to exploit prey patches and highlight the need to fully understand the three-dimensional interactions between predator and prey in the natural environment.
Collapse
|
21
|
|
22
|
DeRuiter SL, Hansen M, Koopman HN, Westgate AJ, Tyack PL, Madsen PT. Propagation of narrow-band-high-frequency clicks: measured and modeled transmission loss of porpoise-like clicks in porpoise habitats. J Acoust Soc Am 2010; 127:560-567. [PMID: 20059001 DOI: 10.1121/1.3257203] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Estimating the range at which harbor porpoises can detect prey items and environmental objects is integral to understanding their biosonar. Understanding the ranges at which they can use echolocation to detect and avoid obstacles is particularly important for strategies to reduce bycatch. Transmission loss (TL) during acoustic propagation is an important determinant of those detection ranges, and it also influences animal detection functions used in passive acoustic monitoring. However, common assumptions regarding TL have rarely been tested. Here, TL of synthetic porpoise clicks was measured in porpoise habitats in Canada and Denmark, and field data were compared with spherical spreading law and ray-trace (Bellhop) model predictions. Both models matched mean observations quite well in most cases, indicating that a spherical spreading law can usually provide an accurate first-order estimate of TL for porpoise sounds in porpoise habitat. However, TL varied significantly (+/-10 dB) between sites and over time in response to variability in seafloor characteristics, sound-speed profiles, and other short-timescale environmental fluctuations. Such variability should be taken into account in estimates of the ranges at which porpoises can communicate acoustically, detect echolocation targets, and be detected via passive acoustic monitoring.
Collapse
Affiliation(s)
- Stacy L DeRuiter
- IFREMER, Service Acoustique et Sismique, BP 70, 29280 Plouzane, France
| | | | | | | | | | | |
Collapse
|
23
|
DeRuiter SL, Bahr A, Blanchet MA, Hansen SF, Kristensen JH, Madsen PT, Tyack PL, Wahlberg M. Acoustic behaviour of echolocating porpoises during prey capture. J Exp Biol 2009; 212:3100-7. [DOI: 10.1242/jeb.030825] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
Porpoise echolocation has been studied previously, mainly in target detection experiments using stationed animals and steel sphere targets, but little is known about the acoustic behaviour of free-swimming porpoises echolocating for prey. Here, we used small onboard sound and orientation recording tags to study the echolocation behaviour of free-swimming trained porpoises as they caught dead, freely drifting fish. We analysed porpoise echolocation behaviour leading up to and following prey capture events,including variability in echolocation in response to vision restriction, prey species, and individual porpoise tested. The porpoises produced echolocation clicks as they searched for the fish, followed by fast-repetition-rate clicks(echolocation buzzes) when acquiring prey. During buzzes, which usually began when porpoises were about 1–2 body lengths from prey, tag-recorded click levels decreased by about 10 dB, click rates increased to over 300 clicks per second, and variability in body orientation (roll) increased. Buzzes generally continued beyond the first contact with the fish, and often extended until or after the end of prey handling. This unexplained continuation of buzzes after prey capture raises questions about the function of buzzes, suggesting that in addition to providing detailed information on target location during the capture, they may serve additional purposes such as the relocation of potentially escaping prey. We conclude that porpoises display the same overall acoustic prey capture behaviour seen in larger toothed whales in the wild,albeit at a faster pace, clicking slowly during search and approach phases and buzzing during prey capture.
Collapse
Affiliation(s)
- Stacy L. DeRuiter
- IFREMER, Service Acoustique et Sismique, B.P. 70, 29280 Plouzané,France
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Alexander Bahr
- Massachusetts Institute of Technology, Center for Ocean Engineering, 32 Vassar Street, Cambridge, MA 02139, USA
| | | | | | | | - Peter T. Madsen
- Department of Biological Sciences, Zoophysiology, Aarhus University, C.F. Møllers Allé, Building 1131, DK-8000 Aarhus C, Denmark
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Peter L. Tyack
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Magnus Wahlberg
- Fjord and Baelt, Margrethes Plads 1, DK-5300 Kerteminde, Denmark
- Marine Biological Laboratory, University of Southern Denmark, Hindsholmsvej 10, 5300 Kerteminde, Denmark
| |
Collapse
|
24
|
DeRuiter SL, Tyack PL, Lin YT, Newhall AE, Lynch JF, Miller PJO. Modeling acoustic propagation of airgun array pulses recorded on tagged sperm whales (Physeter macrocephalus). J Acoust Soc Am 2006; 120:4100-14. [PMID: 17225436 DOI: 10.1121/1.2359705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In 2002 and 2003, tagged sperm whales (Physeter macrocephalus) were experimentally exposed to airgun pulses in the Gulf of Mexico, with the tags providing acoustic recordings at measured ranges and depths. Ray trace and parabolic equation (PE) models provided information about sound propagation paths and accurately predicted time of arrival differences between multipath arrivals. With adequate environmental information, a broadband acoustic PE model predicted the relative levels of multipath arrivals recorded on the tagged whales. However, lack of array source signature data limited modeling of absolute received levels. Airguns produce energy primarily below 250 Hz, with spectrum levels about 20-40 dB lower at 1 kHz. Some arrivals recorded near the surface in 2002 had energy predominantly above 500 Hz; a surface duct in the 2002 sound speed profile helps explain this effect, and the beampattern of the source array also indicates an increased proportion of high-frequency sound at near-horizontal launch angles. These findings indicate that airguns sometimes expose animals to measurable sound energy above 250 Hz, and demonstrate the influences of source and environmental parameters on characteristics of received airgun pulses. The study also illustrates that on-axis source levels and simple geometric spreading inadequately describe airgun pulse propagation and the extent of exposure zones.
Collapse
Affiliation(s)
- Stacy L DeRuiter
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA.
| | | | | | | | | | | |
Collapse
|
25
|
Vojtek AB, Taylor J, DeRuiter SL, Yu JY, Figueroa C, Kwok RPS, Turner DL. Akt regulates basic helix-loop-helix transcription factor-coactivator complex formation and activity during neuronal differentiation. Mol Cell Biol 2003; 23:4417-27. [PMID: 12808085 PMCID: PMC164860 DOI: 10.1128/mcb.23.13.4417-4427.2003] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Neural basic helix-loop-helix (bHLH) transcription factors regulate neurogenesis in vertebrates. Signaling by peptide growth factors also plays critical roles in regulating neuronal differentiation and survival. Many peptide growth factors activate phosphatidylinositol 3-kinase (PI3K) and subsequently the Akt kinases, raising the possibility that Akt may impact bHLH protein function during neurogenesis. Here we demonstrate that reducing expression of endogenous Akt1 and Akt2 by RNA interference (RNAi) reduces neuron generation in P19 cells transfected with a neural bHLH expression vector. The reduction in neuron generation from decreased Akt expression is not solely due to decreased cell survival, since addition of the caspase inhibitor z-VAD-FMK rescues cell death associated with loss of Akt function but does not restore neuron formation. This result indicates that Akt1 and Akt2 have additional functions during neuronal differentiation that are separable from neuronal survival. We show that activated Akt1 enhances complex formation between bHLH proteins and the transcriptional coactivator p300. Activated Akt1 also significantly augments the transcriptional activity of the bHLH protein neurogenin 3 in complex with the coactivators p300 or CBP. In addition, inhibition of endogenous Akt activity by the PI3K/Akt inhibitor LY294002 abolishes transcriptional cooperativity between the bHLH proteins and p300. We propose that Akt regulates the assembly and activity of bHLH-coactivator complexes to promote neuronal differentiation.
Collapse
Affiliation(s)
- Anne B Vojtek
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
Short interfering RNAs (siRNAs) can mediate sequence-specific inhibition of gene expression in mammalian cells. We and others have recently developed expression vector-based systems for synthesizing siRNAs or hairpin siRNAs in mammalian cells. Expression vector-based RNA interference (RNAi) effectively suppresses expression of target genes and is likely to be a powerful tool for analysis of gene function. Here we compare inhibition by vectors expressing hairpin siRNA designs either with different loop sequences connecting the two siRNA strands, or with duplex regions of different lengths. Our results suggest that lengthening the 19-nucleotide duplex region of a relatively ineffective hairpin siRNA can increase inhibition, but increasing the length of an effective 19-nt hairpin siRNA does not increase inhibition. We also demonstrate that hairpin siRNA vectors can be used to inhibit two target genes simultaneously. We have targeted glycogen synthase kinase-3alpha (GSK-3alpha) and GSK-3beta, two related kinases involved in the regulation of a variety of cellular processes and also implicated in the pathogenesis of several human diseases. Inhibition of either GSK-3alpha or GSK-3beta by transfection of hairpin siRNA vectors leads to elevated expression of the GSK-3 target beta-catenin, whereas inhibition of both kinases further increases beta-catenin expression. Our results suggest that vector-based siRNA inhibition may be useful for dissecting the functional roles of GSK-3alpha and GSK-3beta in somatic cells. The ability to inhibit two or more genes simultaneously with hairpin siRNA expression vectors should facilitate studies of gene function in mammalian cells.
Collapse
Affiliation(s)
- Jenn-Yah Yu
- Mental Health Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | | |
Collapse
|
27
|
Abstract
Duplexes of 21-nt RNAs, known as short-interfering RNAs (siRNAs), efficiently inhibit gene expression by RNA interference (RNAi) when introduced into mammalian cells. We show that siRNAs can be synthesized by in vitro transcription with T7 RNA polymerase, providing an economical alternative to chemical synthesis of siRNAs. By using this method, we show that short hairpin siRNAs can function like siRNA duplexes to inhibit gene expression in a sequence-specific manner. Further, we find that hairpin siRNAs or siRNAs expressed from an RNA polymerase III vector based on the mouse U6 RNA promoter can effectively inhibit gene expression in mammalian cells. U6-driven hairpin siRNAs dramatically reduced the expression of a neuron-specific beta-tubulin protein during the neuronal differentiation of mouse P19 cells, demonstrating that this approach should be useful for studies of differentiation and neurogenesis. We also observe that mismatches within hairpin siRNAs can increase the strand selectivity of a hairpin siRNA, which may reduce self-targeting of vectors expressing siRNAs. Use of hairpin siRNA expression vectors for RNAi should provide a rapid and versatile method for assessing gene function in mammalian cells, and may have applications in gene therapy.
Collapse
Affiliation(s)
- Jenn-Yah Yu
- Mental Health Research Institute, Program in Neuroscience, and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109-0669, USA
| | | | | |
Collapse
|