1
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Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Mol Biol Evol 2024; 41:msae036. [PMID: 38376487 PMCID: PMC10919930 DOI: 10.1093/molbev/msae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10×, optical maps, and Hi-C data for scaffolding, polishing, and manual curation. We also provided long read RNA-seq data to facilitate the annotation of the assembly by NCBI and Ensembl. Additionally, we annotated both haplotypes using TOGA and measured the genome size by flow cytometry. We then compared the blue whale genome with other cetaceans and artiodactyls, including vaquita (Phocoena sinus), the world's smallest cetacean, to investigate blue whale's unique biological traits. We found a dramatic amplification of several genes in the blue whale genome resulting from a recent burst in segmental duplications, though the possible connection between this amplification and giant body size requires further study. We also discovered sites in the insulin-like growth factor-1 gene correlated with body size in cetaceans. Finally, using our assembly to examine the heterozygosity and historical demography of Pacific and Atlantic blue whale populations, we found that the genomes of both populations are highly heterozygous and that their genetic isolation dates to the last interglacial period. Taken together, these results indicate how a high-quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.
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Affiliation(s)
- Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Li-Fang Chu
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | | | | | - Daniel Mamott
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Maylie Gonzales
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Cara Argus
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jennifer Bolin
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Mark E Berres
- University of Wisconsin Biotechnology Center, Bioinformatics Resource Center, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
| | - John Steill
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Scott A Swanson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Peng Jiang
- Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH, USA
- Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH, USA
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Robert S Harris
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Bogdan M Kirilenko
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Chetan Munegowda
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Hiller
- LOEWE Centre for Translational Biodiversity Genomics, 60325 Frankfurt, Germany
- Senckenberg Research Institute, 60325 Frankfurt, Germany
- Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Aashish Jain
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Alexander Ionkov
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Kalpana Raja
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
| | - Huishi Toh
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - Aimee Lang
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), La Jolla, CA 92037, USA
| | - Magnus Wolf
- Institute for Evolution and Biodiversity (IEB), University of Muenster, 48149, Muenster, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University/HHMI, New York, NY 10065, USA
| | - James A Thomson
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Ron Stewart
- Regenerative Biology, Morgridge Institute for Research, Madison, WI 53715, USA
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2
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Barlow DR, Klinck H, Ponirakis D, Branch TA, Torres LG. Environmental conditions and marine heatwaves influence blue whale foraging and reproductive effort. Ecol Evol 2023; 13:e9770. [PMID: 36861024 PMCID: PMC9968652 DOI: 10.1002/ece3.9770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 03/01/2023] Open
Abstract
Animal behavior is motivated by the fundamental need to feed and reproduce, and these behaviors can be inferred from spatiotemporal variations in biological signals such as vocalizations. Yet, linking foraging and reproductive effort to environmental drivers can be challenging for wide-ranging predator species. Blue whales are acoustically active marine predators that produce two distinct vocalizations: song and D calls. We examined environmental correlates of these vocalizations using continuous recordings from five hydrophones in the South Taranaki Bight region of Aotearoa New Zealand to investigate call behavior relative to ocean conditions and infer life history patterns. D calls were strongly correlated with oceanographic drivers of upwelling in spring and summer, indicating associations with foraging effort. In contrast, song displayed a highly seasonal pattern with peak intensity in fall, which aligned with the timing of conception inferred from whaling records. Finally, during a marine heatwave, reduced foraging (inferred from D calls) was followed by lower reproductive effort (inferred from song intensity).
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Affiliation(s)
- Dawn R. Barlow
- Geospatial Ecology of Marine Megafauna Lab, Department of Fisheries, Wildlife, and Conservation Sciences, Marine Mammal InstituteOregon State UniversityNewportOregonUSA
| | - Holger Klinck
- K. Lisa Yang Center for Conservation BioacousticsCornell UniversityIthacaNew YorkUSA
- Department of Fisheries, Wildlife, and Conservation Sciences, Marine Mammal InstituteOregon State UniversityNewportOregonUSA
| | - Dimitri Ponirakis
- K. Lisa Yang Center for Conservation BioacousticsCornell UniversityIthacaNew YorkUSA
| | - Trevor A. Branch
- School of Aquatic and Fisheries SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Leigh G. Torres
- Geospatial Ecology of Marine Megafauna Lab, Department of Fisheries, Wildlife, and Conservation Sciences, Marine Mammal InstituteOregon State UniversityNewportOregonUSA
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3
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Barlow DR, Klinck H, Ponirakis D, Holt Colberg M, Torres LG. Temporal occurrence of three blue whale populations in New Zealand waters from passive acoustic monitoring. J Mammal 2022. [DOI: 10.1093/jmammal/gyac106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Describing spatial and temporal occurrence patterns of wild animal populations is important for understanding their evolutionary trajectories, population connectivity, and ecological niche specialization, with relevance for effective management. Throughout the world, blue whales produce stereotyped songs that enable identification of separate acoustic populations. We harnessed continuous acoustic recordings from five hydrophones deployed in the South Taranaki Bight (STB) region of Aotearoa New Zealand from January 2016 to February 2018. We examined hourly presence of songs from three different blue whale populations to investigate their contrasting ecological use of New Zealand waters. The New Zealand song was detected year-round with a seasonal cycle in intensity (peak February–July), demonstrating the importance of the region to the New Zealand population as both a foraging ground and potential breeding area. The Antarctic song was present in two distinct peaks each year (June–July; September–October) and predominantly at the offshore recording locations, suggesting northbound and southbound migration between feeding and wintering grounds. The Australian song was only detected during a 10-day period in January 2017, implying a rare vagrant occurrence. We therefore infer that the STB region is the primary niche of the New Zealand population, a migratory corridor for the Antarctic population, and outside the typical range of the Australian population.
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Affiliation(s)
- Dawn R Barlow
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University , Newport, Oregon 97365 , USA
| | - Holger Klinck
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell University , Ithaca, New York 14850 , USA
- Marine Mammal Institute, Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University , Newport, Oregon 97365 , USA
| | - Dimitri Ponirakis
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell University , Ithaca, New York 14850 , USA
| | - Mattea Holt Colberg
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University , Newport, Oregon 97365 , USA
- Department of Integrative Biology, Oregon State University , Corvallis, Oregon 97331 , USA
| | - Leigh G Torres
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University , Newport, Oregon 97365 , USA
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Barlow DR, Estrada Jorge M, Klinck H, Torres LG. Shaken, not stirred: blue whales show no acoustic response to earthquake events. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220242. [PMID: 35845856 PMCID: PMC9277279 DOI: 10.1098/rsos.220242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Quantifying how animals respond to disturbance events bears relevance for understanding consequences to population health. We investigate whether blue whales respond acoustically to naturally occurring episodic noise by examining calling before and after earthquakes (27 040 calls, 32 earthquakes; 27 January-29 June 2016). Two vocalization types were evaluated: New Zealand blue whale song and downswept vocalizations ('D calls'). Blue whales did not alter the number of D calls, D call received level or song intensity following earthquakes (paired t-tests, p > 0.7 for all). Linear models accounting for earthquake strength and proximity revealed significant relationships between change in calling activity surrounding earthquakes and prior calling activity (D calls: R 2 = 0.277, p < 0.0001; song: R 2 = 0.080, p = 0.028); however, these same relationships were true for 'null' periods without earthquakes (D calls: R 2 = 0.262, p < 0.0001; song: R 2 = 0.149, p = 0.0002), indicating that the pattern is driven by blue whale calling context regardless of earthquake presence. Our findings that blue whales do not respond to episodic natural noise provide context for interpreting documented acoustic responses to anthropogenic noise sources, including shipping traffic and petroleum development, indicating that they potentially evolved tolerance for natural noise sources but not novel noise from anthropogenic origins.
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Affiliation(s)
- Dawn R. Barlow
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, and Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Newport, Oregon, USA
| | - Mateo Estrada Jorge
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, and Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Newport, Oregon, USA
- Department of Computer Science and Department of Physics, Oregon State University, Corvallis, Oregon, USA
| | - Holger Klinck
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell University, Ithaca, New York, USA
- Marine Mammal Institute, Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Newport, Oregon, USA
| | - Leigh G. Torres
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, and Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Newport, Oregon, USA
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5
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Barlow DR, Torres LG. Planning ahead: Dynamic models forecast blue whale distribution with applications for spatial management. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.13992] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dawn R. Barlow
- Geospatial Ecology of Marine Megafauna Lab Department of Fisheries, Wildlife and Conservation Sciences Marine Mammal Institute Oregon State University Newport OR USA
| | - Leigh G. Torres
- Geospatial Ecology of Marine Megafauna Lab Department of Fisheries, Wildlife and Conservation Sciences Marine Mammal Institute Oregon State University Newport OR USA
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6
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Carbaugh-Rutland A, Have Rasmussen J, Sterba-Boatwright B, Širović A. Geographically distinct blue whale song variants in the Northeast Pacific. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Northeast Pacific (NEP) population of blue whales Balaenoptera musculus musculus is currently managed as a single stock. We investigated the fine-scale frequency characteristics of 1 NEP blue whale song unit, the B call. We analyzed B calls from passive acoustic data collected between 2010 and 2013 at 2 low-latitude sites, Palmyra Atoll and the Hawaiian Islands, and 3 higher-latitude sites, off southern California, off Washington state and in the Gulf of Alaska. Frequency measurements were extracted along the contour of the third harmonic from each call, and data from each region were compared. Calls from the Gulf of Alaska and Hawai‘i presented a downshift in frequency, beginning just past the midway point of the contour, which was not present in calls recorded from southern California or Palmyra Atoll. Calls from Washington displayed intermediate characteristics between those from the other 2 high-latitude sites. Cluster analysis resulted in consistent grouping of call contours from Washington and southern California, in what we termed the NEP B1 variant, while contours from Hawai‘i and the Gulf of Alaska were grouped together, as a NEP B2 variant. Frequency differences were also observed among the variants; the Gulf of Alaska displayed the highest frequency on average, followed by Washington, then southern California. Consistent with other studies, a yearly decline in the frequency of B calls was also observed. This discovery of at least 2 geographically distinct variants provides the first evidence of vocally distinct subpopulations within the NEP, indicating the possibility of a need for finer-scale population segmentation.
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Affiliation(s)
- A Carbaugh-Rutland
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77554, USA
| | - J Have Rasmussen
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77554, USA
| | - B Sterba-Boatwright
- College of Science and Engineering, Texas A&M University-Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - A Širović
- Department of Marine Biology, Texas A&M University at Galveston, 200 Seawolf Parkway, Galveston, TX 77554, USA
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Stephenson F, Hewitt JE, Torres LG, Mouton TL, Brough T, Goetz KT, Lundquist CJ, MacDiarmid AB, Ellis J, Constantine R. Cetacean conservation planning in a global diversity hotspot: dealing with uncertainty and data deficiencies. Ecosphere 2021. [DOI: 10.1002/ecs2.3633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Judi E. Hewitt
- National Institute of Water and Atmosphere (NIWA) Hamilton New Zealand
- Department of Statistics University of Auckland Auckland New Zealand
| | - Leigh G. Torres
- Department of Fisheries and Wildlife Marine Mammal Institute Oregon State University Newport Oregon USA
| | - Théophile L. Mouton
- Marine Biodiversity Exploitation, and Conservation (MARBEC) UMR IRD‐CNRS‐UM‐IFREMER 9190 Université de Montpellier Montpellier34095France
| | - Tom Brough
- National Institute of Water and Atmosphere (NIWA) Hamilton New Zealand
| | - Kimberly T. Goetz
- National Oceanic and Atmospheric Administration National Marine Fisheries Service Marine Mammal Laboratory Alaska Fisheries Science Center Seattle Alaska USA
- National Institute of Water and Atmosphere (NIWA) Wellington New Zealand
| | - Carolyn J. Lundquist
- National Institute of Water and Atmosphere (NIWA) Hamilton New Zealand
- Institute of Marine Science University of Auckland Auckland New Zealand
| | | | - Joanne Ellis
- School of Science University of Waikato Tauranga New Zealand
| | - Rochelle Constantine
- Institute of Marine Science University of Auckland Auckland New Zealand
- School of Biological Sciences University of Auckland Auckland New Zealand
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Barlow DR, Klinck H, Ponirakis D, Garvey C, Torres LG. Temporal and spatial lags between wind, coastal upwelling, and blue whale occurrence. Sci Rep 2021; 11:6915. [PMID: 33767285 PMCID: PMC7994810 DOI: 10.1038/s41598-021-86403-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding relationships between physical drivers and biological response is central to advancing ecological knowledge. Wind is the physical forcing mechanism in coastal upwelling systems, however lags between wind input and biological responses are seldom quantified for marine predators. Lags were examined between wind at an upwelling source, decreased temperatures along the upwelling plume's trajectory, and blue whale occurrence in New Zealand's South Taranaki Bight region (STB). Wind speed and sea surface temperature (SST) were extracted for austral spring-summer months between 2009 and 2019. A hydrophone recorded blue whale vocalizations October 2016-March 2017. Timeseries cross-correlation analyses were conducted between wind speed, SST at different locations along the upwelling plume, and blue whale downswept vocalizations (D calls). Results document increasing lag times (0-2 weeks) between wind speed and SST consistent with the spatial progression of upwelling, culminating with increased D call density at the distal end of the plume three weeks after increased wind speeds at the upwelling source. Lag between wind events and blue whale aggregations (n = 34 aggregations 2013-2019) was 2.09 ± 0.43 weeks. Variation in lag was significantly related to the amount of wind over the preceding 30 days, which likely influences stratification. This study enhances knowledge of physical-biological coupling in upwelling ecosystems and enables improved forecasting of species distribution patterns for dynamic management.
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Affiliation(s)
- Dawn R Barlow
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, and Department of Fisheries and Wildlife, Oregon State University, Newport, OR, USA.
| | - Holger Klinck
- Center for Conservation Bioacoustics, Cornell University, Ithaca, NY, USA
- Marine Mammal Institute, Department of Fisheries and Wildlife, Oregon State University, Newport, OR, USA
| | - Dimitri Ponirakis
- Center for Conservation Bioacoustics, Cornell University, Ithaca, NY, USA
| | | | - Leigh G Torres
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, and Department of Fisheries and Wildlife, Oregon State University, Newport, OR, USA
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9
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Nelms SE, Alfaro-Shigueto J, Arnould JPY, Avila IC, Bengtson Nash S, Campbell E, Carter MID, Collins T, Currey RJC, Domit C, Franco-Trecu V, Fuentes MMPB, Gilman E, Harcourt RG, Hines EM, Hoelzel AR, Hooker SK, Johnston DW, Kelkar N, Kiszka JJ, Laidre KL, Mangel JC, Marsh H, Maxwell SM, Onoufriou AB, Palacios DM, Pierce GJ, Ponnampalam LS, Porter LJ, Russell DJF, Stockin KA, Sutaria D, Wambiji N, Weir CR, Wilson B, Godley BJ. Marine mammal conservation: over the horizon. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01115] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Marine mammals can play important ecological roles in aquatic ecosystems, and their presence can be key to community structure and function. Consequently, marine mammals are often considered indicators of ecosystem health and flagship species. Yet, historical population declines caused by exploitation, and additional current threats, such as climate change, fisheries bycatch, pollution and maritime development, continue to impact many marine mammal species, and at least 25% are classified as threatened (Critically Endangered, Endangered or Vulnerable) on the IUCN Red List. Conversely, some species have experienced population increases/recoveries in recent decades, reflecting management interventions, and are heralded as conservation successes. To continue these successes and reverse the downward trajectories of at-risk species, it is necessary to evaluate the threats faced by marine mammals and the conservation mechanisms available to address them. Additionally, there is a need to identify evidence-based priorities of both research and conservation needs across a range of settings and taxa. To that effect we: (1) outline the key threats to marine mammals and their impacts, identify the associated knowledge gaps and recommend actions needed; (2) discuss the merits and downfalls of established and emerging conservation mechanisms; (3) outline the application of research and monitoring techniques; and (4) highlight particular taxa/populations that are in urgent need of focus.
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Affiliation(s)
- SE Nelms
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
| | - J Alfaro-Shigueto
- ProDelphinus, Jose Galvez 780e, Miraflores, Perú
- Facultad de Biologia Marina, Universidad Cientifica del Sur, Lima, Perú
| | - JPY Arnould
- School of Life and Environmental Sciences, Deakin University, Burwood, VIC 3125, Australia
| | - IC Avila
- Grupo de Ecología Animal, Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Cali, Colombia
| | - S Bengtson Nash
- Environmental Futures Research Institute (EFRI), Griffith University, Nathan Campus, 170 Kessels Road, Nathan, QLD 4111, Australia
| | - E Campbell
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
- ProDelphinus, Jose Galvez 780e, Miraflores, Perú
| | - MID Carter
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, UK
| | - T Collins
- Wildlife Conservation Society, 2300 Southern Blvd., Bronx, NY 10460, USA
| | - RJC Currey
- Marine Stewardship Council, 1 Snow Hill, London, EC1A 2DH, UK
| | - C Domit
- Laboratory of Ecology and Conservation, Marine Study Center, Universidade Federal do Paraná, Brazil
| | - V Franco-Trecu
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Uruguay
| | - MMPB Fuentes
- Marine Turtle Research, Ecology and Conservation Group, Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - E Gilman
- Pelagic Ecosystems Research Group, Honolulu, HI 96822, USA
| | - RG Harcourt
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - EM Hines
- Estuary & Ocean Science Center, San Francisco State University, 3150 Paradise Dr. Tiburon, CA 94920, USA
| | - AR Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - SK Hooker
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, UK
| | - DW Johnston
- Duke Marine Lab, 135 Duke Marine Lab Road, Beaufort, NC 28516, USA
| | - N Kelkar
- Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, Karnataka, India
| | - JJ Kiszka
- Department of Biological Sciences, Coastlines and Oceans Division, Institute of Environment, Florida International University, Miami, FL 33199, USA
| | - KL Laidre
- Polar Science Center, APL, University of Washington, 1013 NE 40th Street, Seattle, WA 98105, USA
| | - JC Mangel
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
- ProDelphinus, Jose Galvez 780e, Miraflores, Perú
| | - H Marsh
- James Cook University, Townsville, QLD 48111, Australia
| | - SM Maxwell
- School of Interdisciplinary Arts and Sciences, University of Washington Bothell, Bothell WA 98011, USA
| | - AB Onoufriou
- School of Biology, University of St Andrews, Fife, KY16 8LB, UK
- Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - DM Palacios
- Marine Mammal Institute, Hatfield Marine Science Center, Oregon State University, Newport, OR, 97365, USA
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR 97330, USA
| | - GJ Pierce
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
- Instituto de Investigaciones Marinas, Consejo Superior de Investigaciones Cientificas, Eduardo Cabello 6, 36208 Vigo, Pontevedra, Spain
| | - LS Ponnampalam
- The MareCet Research Organization, 40460 Shah Alam, Malaysia
| | - LJ Porter
- SMRU Hong Kong, University of St. Andrews, Hong Kong
| | - DJF Russell
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, Fife, KY16 8LB, UK
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Fife, KY16 8LB, UK
| | - KA Stockin
- Animal Welfare Science and Bioethics Centre, School of Veterinary Science, Massey University, Private Bag 11-222, Palmerston North, New Zealand
| | - D Sutaria
- School of Interdisciplinary Arts and Sciences, University of Washington Bothell, Bothell WA 98011, USA
| | - N Wambiji
- Kenya Marine and Fisheries Research Institute, P.O. Box 81651, Mombasa-80100, Kenya
| | - CR Weir
- Ketos Ecology, 4 Compton Road, Kingsbridge, Devon, TQ7 2BP, UK
| | - B Wilson
- Scottish Association for Marine Science, Oban, Argyll, PA37 1QA, UK
| | - BJ Godley
- Centre for Ecology and Conservation, University of Exeter, Cornwall, TR10 9EZ, UK
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Warren VE, McPherson C, Giorli G, Goetz KT, Radford CA. Marine soundscape variation reveals insights into baleen whales and their environment: a case study in central New Zealand. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201503. [PMID: 33959320 PMCID: PMC8074962 DOI: 10.1098/rsos.201503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
Baleen whales reliably produce stereotyped vocalizations, enabling their spatio-temporal distributions to be inferred from acoustic detections. Soundscape analysis provides an integrated approach whereby vocal species, such as baleen whales, are sampled holistically with other acoustic contributors to their environment. Acoustic elements that occur concurrently in space, time and/or frequency can indicate overlaps between free-ranging species and potential stressors. Such information can inform risk assessment framework models. Here, we demonstrate the utility of soundscape monitoring in central New Zealand, an area of high cetacean diversity where potential threats are poorly understood. Pygmy blue whale calls were abundant in the South Taranaki Bight (STB) throughout recording periods and were also detected near Kaikōura during autumn. Humpback, Antarctic blue and Antarctic minke whales were detected in winter and spring, during migration. Wind, rain, tidal and wave activity increased ambient sound levels in both deep- and shallow-water environments across a broad range of frequencies, including those used by baleen whales, and sound from shipping, seismic surveys and earthquakes overlapped in time, space and frequency with whale calls. The results highlight the feasibility of soundscape analysis to quantify and understand potential stressors to free-ranging species, which is essential for conservation and management decisions.
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Affiliation(s)
- Victoria E. Warren
- Institute of Marine Science, Leigh Marine Laboratory, University of Auckland, 160 Goat Island Road, Leigh 0985, New Zealand
- National Institute of Water and Atmospheric Research, 301 Evans Bay Parade, Hataitai, Wellington 6021, New Zealand
| | - Craig McPherson
- JASCO Applied Sciences (Australia) Pty Ltd, 14 Hook Street, Unit 1, Capalaba QLD 4157, Australia
| | - Giacomo Giorli
- National Institute of Water and Atmospheric Research, 301 Evans Bay Parade, Hataitai, Wellington 6021, New Zealand
| | - Kimberly T. Goetz
- National Institute of Water and Atmospheric Research, 301 Evans Bay Parade, Hataitai, Wellington 6021, New Zealand
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, National Marine Mammal Laboratory, 7600 Sand Point Way NE, Seattle, WA 98115, USA
| | - Craig A. Radford
- Institute of Marine Science, Leigh Marine Laboratory, University of Auckland, 160 Goat Island Road, Leigh 0985, New Zealand
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Movements and behaviour of blue whales satellite tagged in an Australian upwelling system. Sci Rep 2020; 10:21165. [PMID: 33273533 PMCID: PMC7713308 DOI: 10.1038/s41598-020-78143-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/10/2020] [Indexed: 11/15/2022] Open
Abstract
Knowledge about the movement ecology of endangered species is needed to identify biologically important areas and the spatio-temporal scale of potential human impacts on species. Blue whales (Balaenoptera musculus) are endangered due to twentieth century whaling and currently threatened by human activities. In Australia, they feed in the Great Southern Australian Coastal Upwelling System (GSACUS) during the austral summer. We investigate their movements, occupancy, behaviour, and environmental drivers to inform conservation management. Thirteen whales were satellite tagged, biopsy sampled and photo-identified in 2015. All were genetically confirmed to be of the pygmy subspecies (B. m. brevicauda). In the GSACUS, whales spent most of their time over the continental shelf and likely foraging in association with several seascape variables (sea surface temperature variability, depth, wind speed, sea surface height anomaly, and chlorophyll a). When whales left the region, they migrated west and then north along the Australian coast until they reached West Timor and Indonesia, where their movements indicated breeding or foraging behaviour. These results highlight the importance of the GSACUS as a foraging ground for pygmy blue whales inhabiting the eastern Indian Ocean and indicate the whales’ migratory route to proposed breeding grounds off Indonesia. Information about the spatio-temporal scale of potential human impacts can now be used to protect this little-known subspecies of blue whale.
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12
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Torres LG, Barlow DR, Chandler TE, Burnett JD. Insight into the kinematics of blue whale surface foraging through drone observations and prey data. PeerJ 2020; 8:e8906. [PMID: 32351781 PMCID: PMC7183305 DOI: 10.7717/peerj.8906] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/12/2020] [Indexed: 11/20/2022] Open
Abstract
To understand how predators optimize foraging strategies, extensive knowledge of predator behavior and prey distribution is needed. Blue whales employ an energetically demanding lunge feeding method that requires the whales to selectively feed where energetic gain exceeds energetic loss, while also balancing oxygen consumption, breath holding capacity, and surface recuperation time. Hence, blue whale foraging behavior is primarily driven by krill patch density and depth, but many studies have not fully considered surface feeding as a significant foraging strategy in energetic models. We collected predator and prey data on a blue whale (Balaenoptera musculus brevicauda) foraging ground in New Zealand in February 2017 to assess the distributional and behavioral response of blue whales to the distribution and density of krill prey aggregations. Krill density across the study region was greater toward the surface (upper 20 m), and blue whales were encountered where prey was relatively shallow and more dense. This relationship was particularly evident where foraging and surface lunge feeding were observed. Furthermore, New Zealand blue whales also had relatively short dive times (2.83 ± 0.27 SE min) as compared to other blue whale populations, which became even shorter at foraging sightings and where surface lunge feeding was observed. Using an unmanned aerial system (UAS; drone) we also captured unique video of a New Zealand blue whale's surface feeding behavior on well-illuminated krill patches. Video analysis illustrates the whale's potential use of vision to target prey, make foraging decisions, and orient body mechanics relative to prey patch characteristics. Kinematic analysis of a surface lunge feeding event revealed biomechanical coordination through speed, acceleration, head inclination, roll, and distance from krill patch to maximize prey engulfment. We compared these lunge kinematics to data previously reported from tagged blue whale lunges at depth to demonstrate strong similarities, and provide rare measurements of gape size, and krill response distance and time. These findings elucidate the predator-prey relationship between blue whales and krill, and provide support for the hypothesis that surface feeding by New Zealand blue whales is an important component to their foraging ecology used to optimize their energetic efficiency. Understanding how blue whales make foraging decisions presents logistical challenges, which may cause incomplete sampling and biased ecological knowledge if portions of their foraging behavior are undocumented. We conclude that surface foraging could be an important strategy for blue whales, and integration of UAS with tag-based studies may expand our understanding of their foraging ecology by examining surface feeding events in conjunction with behaviors at depth.
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Affiliation(s)
- Leigh G. Torres
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, Department of Fisheries and Wildlife, Oregon State University, Newport, OR, United States of America
| | - Dawn R. Barlow
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, Department of Fisheries and Wildlife, Oregon State University, Newport, OR, United States of America
| | - Todd E. Chandler
- Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, Oregon State University, Newport, OR, United States of America
| | - Jonathan D. Burnett
- Aerial Information Systems Laboratory, Forest Engineering, Resources and Management, Oregon State University, Corvallis, OR, United States of America
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Stephenson F, Goetz K, Sharp BR, Mouton TL, Beets FL, Roberts J, MacDiarmid AB, Constantine R, Lundquist CJ. Modelling the spatial distribution of cetaceans in New Zealand waters. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13035] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Fabrice Stephenson
- National Institute of Water and Atmospheric Research (NIWA) Hamilton New Zealand
| | - Kimberly Goetz
- National Institute of Water and Atmospheric Research (NIWA) Wellington New Zealand
| | - Ben R. Sharp
- Fisheries New Zealand Ministry for Primary Industries Wellington New Zealand
| | - Théophile L. Mouton
- Marine Biodiversity, Exploitation, and Conservation (MARBEC) UMR 9190 Université de Montpellier Montpellier France
| | - Fenna L. Beets
- National Institute of Water and Atmospheric Research (NIWA) Hamilton New Zealand
| | - Jim Roberts
- National Institute of Water and Atmospheric Research (NIWA) Wellington New Zealand
| | - Alison B. MacDiarmid
- National Institute of Water and Atmospheric Research (NIWA) Wellington New Zealand
| | - Rochelle Constantine
- School of Biological Sciences University of Auckland Auckland New Zealand
- Institute of Marine Science University of Auckland Auckland New Zealand
| | - Carolyn J. Lundquist
- National Institute of Water and Atmospheric Research (NIWA) Hamilton New Zealand
- Institute of Marine Science University of Auckland Auckland New Zealand
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Leroy EC, Samaran F, Stafford KM, Bonnel J, Royer JY. Broad-scale study of the seasonal and geographic occurrence of blue and fin whales in the Southern Indian Ocean. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00927] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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