1
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Cosentino M, Marcolin C, Griffiths ET, Sánchez-Camí E, Tougaard J. Dolphin and porpoise detections by the F-POD are not independent: Implications for sympatric species monitoring. JASA EXPRESS LETTERS 2024; 4:031202. [PMID: 38467471 DOI: 10.1121/10.0025304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
The F-POD is designed for passive acoustic monitoring of odontocetes. The offline classifiers can identify and separate porpoise-like sounds from dolphin-like sounds. We show that these two classifiers are not working independently. Run together, virtually no detections of both species were reported within the same minute, whereas 10% of the detection positive minutes were reported positive for both species when the two classifiers were run sequentially. This has important implications for interpretation of data in areas containing both species groups, and we call for reporting all analysis details in such studies and for further description and analysis of the classifiers.
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Affiliation(s)
- Mel Cosentino
- Department of Ecoscience, Aarhus University, 8000 Aarhus, , , , ,
| | | | | | | | - Jakob Tougaard
- Department of Ecoscience, Aarhus University, 8000 Aarhus, , , , ,
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2
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Rojas-Bracho L, Taylor B, Booth C, Thomas L, Jaramillo-Legorreta A, Nieto-García E, Cárdenas Hinojosa G, Barlow J, Mesnick SL, Gerrodette T, Olson P, Henry A, Rizo H, Hidalgo-Pla E, Bonilla-Garzón A. More vaquita porpoises survive than expected. ENDANGER SPECIES RES 2022. [DOI: 10.3354/esr01197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In 2018, it was estimated that fewer than 20 of Mexico’s endemic vaquita porpoise Phocoena sinus remained, and the species was declining by 47% yr-1. Entanglement in gillnets is the sole threat to the species, and since the last population size estimate, gillnetting has increased in the small area where most vaquitas remain—a 12 × 24 km area in the Gulf of California near San Felipe, Mexico. We conducted research efforts in 2019 and 2021 in that area to estimate the minimum numbers of adults and calves and look for any signs that vaquitas are unhealthy. Through expert elicitation, we estimated between 7 and 15 unique individuals were seen in 2019 and 5-13 were seen in 2021. Calves were seen in both years, and all vaquitas appeared healthy. Population projections from the last full survey indicated that more vaquitas have survived than expected. We suggest that these surviving adult vaquitas may have learned to avoid entanglement in gillnets. These vaquitas and their calves provide hope that the species can survive. However, given the high levels of illegal gillnetting and the theft of equipment which hindered our monitoring efforts, and with only around 10 individuals remaining, survival can only be assured if vaquita habitat is made gillnet-free.
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Affiliation(s)
- L Rojas-Bracho
- PNUD/Sinergiaen en la Comisión Nacional de Áreas Naturales Protegidas, Ensenada, BC, México
| | - B Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA
| | - C Booth
- SMRU Consulting, St Andrews, Fife KY16 8LB, UK
| | - L Thomas
- Centre for Research into Ecological and Environmental Modelling, University of St Andrews, St Andrews, Fife KY16 9LZ, UK
| | | | - E Nieto-García
- Comisión Natural de Áreas Naturales Protegidas, Ensenada, BC, México
| | | | - J Barlow
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA
| | - SL Mesnick
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA
| | - T Gerrodette
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA
| | - P Olson
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA
| | - A Henry
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA 92037, USA
| | - H Rizo
- Museo de la Ballena y Ciencias del Mar, La Paz, BC 23000, México
| | - E Hidalgo-Pla
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92037, USA
| | - A Bonilla-Garzón
- K. Lisa Yang Center for Conservation Bioacoustics, Ithaca, NY 14850, USA
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3
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Macaulay J, Kingston A, Coram A, Oswald M, Swift R, Gillespie D, Northridge S. Passive acoustic tracking of the three‐dimensional movements and acoustic behaviour of toothed whales in close proximity to static nets. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jamie Macaulay
- Sea Mammal Research Unit Scottish Oceans Institute Scotland, UK
| | - Al Kingston
- Sea Mammal Research Unit Scottish Oceans Institute Scotland, UK
| | - Alex Coram
- Sea Mammal Research Unit Scottish Oceans Institute Scotland, UK
| | - Michael Oswald
- Sea Mammal Research Unit Scottish Oceans Institute Scotland, UK
| | - René Swift
- Sea Mammal Research Unit Scottish Oceans Institute Scotland, UK
| | - Doug Gillespie
- Sea Mammal Research Unit Scottish Oceans Institute Scotland, UK
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4
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Ladegaard M, Macaulay J, Simon M, Laidre KL, Mitseva A, Videsen S, Pedersen MB, Tougaard J, Madsen PT. Soundscape and ambient noise levels of the Arctic waters around Greenland. Sci Rep 2021; 11:23360. [PMID: 34862381 PMCID: PMC8642542 DOI: 10.1038/s41598-021-02255-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/27/2021] [Indexed: 11/09/2022] Open
Abstract
A longer Arctic open water season is expected to increase underwater noise levels due to anthropogenic activities such as shipping, seismic surveys, sonar, and construction. Many Arctic marine mammal species depend on sound for communication, navigation, and foraging, therefore quantifying underwater noise levels is critical for documenting change and providing input to management and legislation. Here we present long-term underwater sound recordings from 26 deployments around Greenland from 2011 to 2020. Ambient noise was analysed in third octave and decade bands and further investigated using generic detectors searching for tonal and transient sounds. Ambient noise levels partly overlap with previous Arctic observations, however we report much lower noise levels than previously documented, specifically for Melville Bay and the Greenland Sea. Consistent seasonal noise patterns occur in Melville Bay, Baffin Bay and Greenland Sea, with noise levels peaking in late summer and autumn correlating with open water periods and seismic surveys. These three regions also had similar tonal detection patterns that peaked in May/June, likely due to bearded seal vocalisations. Biological activity was more readily identified using detectors rather than band levels. We encourage additional research to quantify proportional noise contributions from geophysical, biological, and anthropogenic sources in Arctic waters.
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Affiliation(s)
- Michael Ladegaard
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark.
| | - Jamie Macaulay
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Malene Simon
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Greenland Climate Research Centre, Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Kristin L Laidre
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA, USA
| | | | - Simone Videsen
- Zoophysiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Jakob Tougaard
- Marine Mammal Research, Department of Ecoscience, Aarhus University, Roskilde, Denmark
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5
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Romeu B, Machado AMS, Daura-Jorge FG, Cremer MJ, de Moraes Alves AK, Simões-Lopes PC. Low-frequency sampling rates are effective to record bottlenose dolphins. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201598. [PMID: 34350008 PMCID: PMC8316790 DOI: 10.1098/rsos.201598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Acoustic monitoring in cetacean studies is an effective but expensive approach. This is partly because of the high sampling rate required by acoustic devices when recording high-frequency echolocation clicks. However, the proportion of echolocation clicks recorded at different frequencies is unknown for many species, including bottlenose dolphins. Here, we investigated the echolocation clicks of two subspecies of bottlenose dolphins in the western South Atlantic Ocean. The possibility of recording echolocation clicks at 24 and 48 kHz was assessed by two approaches. First, we considered the clicks in the frequency range up to 96 kHz. We found a loss of 0.95-13.90% of echolocation clicks in the frequency range below 24 kHz, and 0.01-0.42% below 48 kHz, to each subspecies. Then, we evaluated these recordings downsampled at 48 and 96 kHz and confirmed that echolocation clicks are recorded at these lower frequencies, with some loss. Therefore, despite reaching high frequencies, the clicks can also be recorded at lower frequencies because echolocation clicks from bottlenose dolphins are broadband. We concluded that ecological studies based on the presence-absence data are still effective for bottlenose dolphins when acoustic devices with a limited sampling rate are used.
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Affiliation(s)
- Bianca Romeu
- Laboratório de Mamíferos Aquáticos, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Programa de Pós-Graduação em Ecologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Alexandre M. S. Machado
- Laboratório de Mamíferos Aquáticos, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Programa de Pós-Graduação em Ecologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Department of Collective Behaviour, Max Planck Institute of Animal Behaviour, Konstanz, Germany
| | - Fábio G. Daura-Jorge
- Laboratório de Mamíferos Aquáticos, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Programa de Pós-Graduação em Ecologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Marta J. Cremer
- Programa de Pós-Graduação em Ecologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Programa de Pós-Graduação em Saúde e Meio Ambiente, Universidade da Região de Joinville, Joinville, Brazil
- Laboratório de Ecologia e Conservação de Tetrápodes Marinhos e Costeiros, Universidade da Região de Joinville, Joinville, Brazil
| | - Ana Kássia de Moraes Alves
- Laboratório de Ecologia e Conservação de Tetrápodes Marinhos e Costeiros, Universidade da Região de Joinville, Joinville, Brazil
| | - Paulo C. Simões-Lopes
- Laboratório de Mamíferos Aquáticos, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Programa de Pós-Graduação em Ecologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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6
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McGowen MR, Tsagkogeorga G, Álvarez-Carretero S, Dos Reis M, Struebig M, Deaville R, Jepson PD, Jarman S, Polanowski A, Morin PA, Rossiter SJ. Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture. Syst Biol 2020; 69:479-501. [PMID: 31633766 PMCID: PMC7164366 DOI: 10.1093/sysbio/syz068] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 10/02/2019] [Accepted: 10/06/2019] [Indexed: 12/20/2022] Open
Abstract
The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for \documentclass[12pt]{minimal}
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}{}$\sim $\end{document}3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from \documentclass[12pt]{minimal}
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}{}$>$\end{document}38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.]
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Affiliation(s)
- Michael R McGowen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.,Department of Vertebrate Zoology, Smithsonian Museum of Natural History, 10th & Constitution Ave. NW, Washington DC 20560, USA
| | - Georgia Tsagkogeorga
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Sandra Álvarez-Carretero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Monika Struebig
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Robert Deaville
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Paul D Jepson
- Institute of Zoology, Zoological Society of London, Outer Circle, London NW1 4RY, UK
| | - Simon Jarman
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Perth WA 6009, Australia
| | - Andrea Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston TAS 7050, Australia
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla CA 92037 USA
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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7
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Morin PA, Archer FI, Avila CD, Balacco JR, Bukhman YV, Chow W, Fedrigo O, Formenti G, Fronczek JA, Fungtammasan A, Gulland FMD, Haase B, Peter Heide-Jorgensen M, Houck ML, Howe K, Misuraca AC, Mountcastle J, Musser W, Paez S, Pelan S, Phillippy A, Rhie A, Robinson J, Rojas-Bracho L, Rowles TK, Ryder OA, Smith CR, Stevenson S, Taylor BL, Teilmann J, Torrance J, Wells RS, Westgate AJ, Jarvis ED. Reference genome and demographic history of the most endangered marine mammal, the vaquita. Mol Ecol Resour 2020; 21:1008-1020. [PMID: 33089966 PMCID: PMC8247363 DOI: 10.1111/1755-0998.13284] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/08/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Catherine D Avila
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Jennifer R Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, USA
| | | | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Julie A Fronczek
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | - Marlys L Houck
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | - Ann C Misuraca
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - Sadye Paez
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | | | - Adam Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | | | - Teri K Rowles
- Office of Protected Resources, National Marine Fisheries Service, NOAA, Silver Spring, MD, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Jonas Teilmann
- Marine Mammal Research, Department of Bioscience, Aarhus University, Roskilde, Denmark
| | | | - Randall S Wells
- Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | | | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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8
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Lam SS, Chew KW, Show PL, Ma NL, Ok YS, Peng W, Alstrup AKO, Adams DH, Rinklebe J, Sonne C. Environmental management of two of the world's most endangered marine and terrestrial predators: Vaquita and cheetah. ENVIRONMENTAL RESEARCH 2020; 190:109966. [PMID: 32829186 DOI: 10.1016/j.envres.2020.109966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Two of the world most endangered marine and terrestrial species are at the brink of extinction. The vaquita (Phocoena sinus) is the smallest existing cetacean and the population has declined to barely 22 individuals now remaining in Mexico's Gulf of California. With the ongoing decline, it is likely to go extinct within few years. The primary threat to this species has been mortality as a result of by-catch from gillnet fishing as well as environmental toxic chemicals and disturbance. This has called for the need to establish a National Park within the Gulf of California to expand essential habitat and provide the critical ecosystem protection for vaquita to thrive and multiply, given that proper conservation enforcement and management of the park are accomplished. In the terrestrial environment, the cheetah (Acinonyx jubatus) is reduced to a low number worldwide with the Iran subpopulation currently listed as Critically Endangered and the Indian subpopulation already extinct. There is a need for conservation efforts due to habitat loss, but also an indication of the conspicuous threat of illegal trade and trafficking from Africa and Arab countries in the Middle East. Funds have also been set up to provide refuges for the cheetah by working directly with farmers and landowners, which is a critical movement in adaptive management. These are the potential options for the preservation and possibly the expansion of the overall vaquita and cheetah populations.
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Affiliation(s)
- Su Shiung Lam
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; Pyrolysis Technology Research Group, Institute of Tropical Aquaculture and Fisheries (AKUATROP), Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Kit Wayne Chew
- School of Energy and Chemical Engineering, Xiamen University Malaysia, Jalan Sunsuria, Bandar Sunsuria, 43900, Sepang, Selangor, Malaysia
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Nyuk Ling Ma
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; Faculty of Science & Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Yong Sik Ok
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; Korea Biochar Research Center & Division of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Wanxi Peng
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Aage K O Alstrup
- Aarhus University Hospital, Department of Nuclear Medicine and PET, Palle Juul-Jensens Boulevard 99, DK-8200, Aarhus, Denmark
| | - Douglas H Adams
- Cape Canaveral Scientific, 220 Surf Road, Melbourne Beach, Florida, 32951, USA
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Soil- and Groundwater-Management, Pauluskirchstraße 7, 42285, Wuppertal, Germany; Department of Environment, Energy, and Geoinformatics, Sejong University, Seoul, 05006, Republic of Korea
| | - Christian Sonne
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou, 450002, China; Department of Bioscience, Arctic Research Centre (ARC), Aarhus University, Faculty of Science and Technology, Frederiksborgvej 399, PO Box 358, DK-4000, Roskilde, Denmark.
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9
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Ben Chehida Y, Thumloup J, Schumacher C, Harkins T, Aguilar A, Borrell A, Ferreira M, Rojas-Bracho L, Robertson KM, Taylor BL, Víkingsson GA, Weyna A, Romiguier J, Morin PA, Fontaine MC. Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum. Sci Rep 2020; 10:15190. [PMID: 32938978 PMCID: PMC7494866 DOI: 10.1038/s41598-020-71603-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023] Open
Abstract
Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.
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Affiliation(s)
- Yacine Ben Chehida
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Julie Thumloup
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands
| | - Cassie Schumacher
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Timothy Harkins
- Swift Biosciences, 674 S. Wagner Rd., Suite 100, Ann Arbor, MI, 48103, USA
| | - Alex Aguilar
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Asunción Borrell
- IRBIO and Department of Evolutive Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Diagonal 643, 08071, Barcelona, Spain
| | - Marisa Ferreira
- MATB-Sociedade Portuguesa de Vida Selvagem, Estação de Campo de Quiaios, Apartado EC Quiaios, 3080-530, Figueira da Foz, Portugal.,CPRAM-Ecomare, Estrada Do Porto de Pesca Costeira, 3830-565, Gafanha da Nazaré, Portugal
| | - Lorenzo Rojas-Bracho
- Comisión Nacional de Áreas Naturales Protegidas (CONANP), C/o Centro de Investigación Científica y de Educación Superior de Ensenada, Carretera Ensenada-Tijuana 3918, Fraccionamiento Zona Playitas, 22860, Ensenada, BC, Mexico
| | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Gísli A Víkingsson
- Marine and Freshwater Research Institute, Fornubúðum 5, 220, Hafnarfjörður, Iceland
| | - Arthur Weyna
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Jonathan Romiguier
- Institut Des Sciences de L'Évolution (Université de Montpellier, CNRS UMR 5554), Montpellier, France
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 8901 La Jolla Shores Dr., La Jolla, CA, 92037, USA
| | - Michael C Fontaine
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, The Netherlands. .,Laboratoire MIVEGEC (Université de Montpellier, CNRS 5290, IRD 229) et Centre de Recherche en Écologie et Évolution de la Santé (CREES), Institut de Recherche Pour Le Développement (IRD), 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France.
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10
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Cárdenas Hinojosa G, de la Cueva H, Gerrodette T, Jaramillo-Legorreta AM. Distribution of the acoustic occurrence of dolphins during the summers 2011 to 2015 in the Upper Gulf of California, Mexico. PeerJ 2020; 8:e9121. [PMID: 32509451 PMCID: PMC7245336 DOI: 10.7717/peerj.9121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/13/2020] [Indexed: 11/20/2022] Open
Abstract
Baseline knowledge of spatial and temporal distribution patterns is essential for cetacean management and conservation. Such knowledge is particularly important in areas where gillnet fishing occurs, as the Upper Gulf of California, which increases the probability of bycatch of cetaceans. In this area, the vaquita porpoise (Phocoena sinus) has been widely studied, but the knowledge of other cetaceans is scarce and based on traditional visual survey methods. We used data collected by an array of acoustic click detectors (C-PODs) during the summers 2011 to 2015 to analyze the distribution of dolphins in the Vaquita Refuge in the Upper Gulf of California. We recorded 120,038 echolocation click trains of dolphins during 12,371 days of recording effort at 46 sampling sites. Based on simultaneous visual and acoustic data, we estimated a false positive acoustic detection rate of 19.4%. Dolphin acoustic activity varied among sites, with higher activity in the east of the Vaquita Refuge. Acoustic activity was higher at night than during the day. We used negative binomial generalized linear models to study the count of clicks of dolphins in relation to spatial, temporal, physical, biological and anthropogenic explanatory variables. The best model selected for the response variable included sampling site, day-night condition, and vertical component of tide speed. Patterns in the spatial distribution of predicted acoustic activity of dolphins were similar to the acoustic activity observed per sampling season. Higher acoustic activity was predicted at night, but the tide speed variable was not relevant under this condition. Acoustic activity patterns could be related to the availability of prey resources since echolocation click trains are associated with foraging activities of dolphins. This is the first study of the distribution of dolphins in Mexico using medium-term systematic passive acoustic monitoring, and the results can contribute to better management to the natural protected area located in the Upper Gulf of California.
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Affiliation(s)
- Gustavo Cárdenas Hinojosa
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, México.,Comisión Nacional de Áreas Naturales Protegidas, Secretaría de Medio Ambiente y Recursos Naturales, Ensenada, Baja California, México
| | - Horacio de la Cueva
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, México
| | - Tim Gerrodette
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, San Diego, CA, United States of America
| | - Armando M Jaramillo-Legorreta
- Comisión Nacional de Áreas Naturales Protegidas, Secretaría de Medio Ambiente y Recursos Naturales, Ensenada, Baja California, México
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11
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Brownell Jr RL, Reeves RR, Read AJ, Smith BD, Thomas PO, Ralls K, Amano M, Berggren P, Chit AM, Collins T, Currey R, Dolar MLL, Genov T, Hobbs RC, Kreb D, Marsh H, Zhigang M, Perrin WF, Phay S, Rojas-Bracho L, Ryan GE, Shelden KEW, Slooten E, Taylor BL, Vidal O, Ding W, Whitty TS, Wang JY. Bycatch in gillnet fisheries threatens Critically Endangered small cetaceans and other aquatic megafauna. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00994] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Dunch V. Saving the vaquita one bite at a time: The missing role of the shrimp consumer in vaquita conservation. MARINE POLLUTION BULLETIN 2019; 145:583-586. [PMID: 31590827 DOI: 10.1016/j.marpolbul.2019.06.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 05/20/2019] [Accepted: 06/16/2019] [Indexed: 06/10/2023]
Abstract
The vaquita (Phocoena sinus) is the world's smallest cetacean and most endangered marine mammal. The species is under threat from illegal fishing activities that take place in the upper Gulf of California (UGC). Artisanal use of gillnets to catch shrimp and poach the endangered totoaba are the primary drivers of vaquita population declines due to bycatch. About 80% of shrimp caught in the UGC is sold to the United States, meaning Americans who consume shrimp may have a direct connection to the plight of the critically endangered vaquita. However, this issue as part of the human dimensions of vaquita conservation has been largely unstudied. Additionally, the majority of Americans are unfamiliar with the vaquita which hinders conservation efforts. This article calls for further research into the human dimensions of vaquita conservation, increased collaboration with fishing communities in the UGC, and connecting seafood sellers and consumers with the vaquita crisis.
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Affiliation(s)
- Victoria Dunch
- Miami University, Department of Biology, Project Dragonfly, 701 Western College Dr, Oxford, OH 45056, United States of America.
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13
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Jaramillo-Legorreta AM, Cardenas-Hinojosa G, Nieto-Garcia E, Rojas-Bracho L, Thomas L, Ver Hoef JM, Moore J, Taylor B, Barlow J, Tregenza N. Decline towards extinction of Mexico's vaquita porpoise ( Phocoena sinus). ROYAL SOCIETY OPEN SCIENCE 2019; 6:190598. [PMID: 31417757 PMCID: PMC6689580 DOI: 10.1098/rsos.190598] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
The vaquita (Phocoena sinus) is a small porpoise endemic to Mexico. It is listed by IUCN as Critically Endangered because of unsustainable levels of bycatch in gillnets. The population has been monitored with passive acoustic detectors every summer from 2011 to 2018; here we report results for 2017 and 2018. We combine the acoustic trends with an independent estimate of population size from 2015, and visual observations of at least seven animals in 2017 and six in 2018. Despite adoption of an emergency gillnet ban in May 2015, the estimated rate of decline remains extremely high: 48% decline in 2017 (95% Bayesian credible interval (CRI) 78% decline to 9% increase) and 47% in 2018 (95% CRI 80% decline to 13% increase). Estimated total population decline since 2011 is 98.6%, with greater than 99% probability the decline is greater than 33% yr-1. We estimate fewer than 19 vaquitas remained as of summer 2018 (posterior mean 9, median 8, 95% CRI 6-19). From March 2016 to March 2019, 10 dead vaquitas killed in gillnets were found. The ongoing presence of illegal gillnets despite the emergency ban continues to drive the vaquita towards extinction. Immediate management action is required if the species is to be saved.
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Affiliation(s)
- Armando M. Jaramillo-Legorreta
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, CICESE Camper 10, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California 22860, Mexico
| | - Gustavo Cardenas-Hinojosa
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, CICESE Camper 10, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California 22860, Mexico
| | - Edwyna Nieto-Garcia
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, CICESE Camper 10, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California 22860, Mexico
| | - Lorenzo Rojas-Bracho
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, CICESE Camper 10, Carretera Ensenada-Tijuana 3918, Zona Playitas, Ensenada, Baja California 22860, Mexico
| | - Len Thomas
- Centre for Research into Ecological and Environmental Modelling, The Observatory, Buchanan Gardens, University of St Andrews, St Andrews, Fife KY16 9LZ, UK
| | - Jay M. Ver Hoef
- Alaska Fisheries Science Center, NOAA Fisheries, Marine Mammal Laboratory, Seattle, WA 98115, USA
| | - Jeffrey Moore
- Southwest Fisheries Science Center, NOAA Fisheries, Marine Mammal and Turtle Division, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
| | - Barbara Taylor
- Southwest Fisheries Science Center, NOAA Fisheries, Marine Mammal and Turtle Division, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
| | - Jay Barlow
- Southwest Fisheries Science Center, NOAA Fisheries, Marine Mammal and Turtle Division, 8901 La Jolla Shores Drive, La Jolla, CA 92037, USA
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14
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Rojas-Bracho L, Gulland FMD, Smith CR, Taylor B, Wells RS, Thomas PO, Bauer B, Heide-Jørgensen MP, Teilmann J, Dietz R, Balle JD, Jensen MV, Sinding MHS, Jaramillo-Legorreta A, Abel G, Read AJ, Westgate AJ, Colegrove K, Gomez F, Martz K, Rebolledo R, Ridgway S, Rowles T, van Elk CE, Boehm J, Cardenas-Hinojosa G, Constandse R, Nieto-Garcia E, Phillips W, Sabio D, Sanchez R, Sweeney J, Townsend F, Vivanco J, Vivanco JC, Walker S. A field effort to capture critically endangered vaquitas Phocoena sinus for protection from entanglement in illegal gillnets. ENDANGER SPECIES RES 2019. [DOI: 10.3354/esr00931] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Rojas-Bracho L, Brusca RC, Álvarez-Borrego S, Brownell RL, Camacho-Ibar V, Ceballos G, de la Cueva H, García-Hernández J, Hastings PA, Cárdenas-Hinojosa G, Jaramillo-Legorreta AM, Medellín R, Mesnick SL, Nieto-García E, Urbán J, Velarde E, Vidal O, Findley LT, Taylor BL. Unsubstantiated Claims Can Lead to Tragic Conservation Outcomes. Bioscience 2019; 69:12-14. [PMID: 30647475 PMCID: PMC6327833 DOI: 10.1093/biosci/biy138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Saúl Álvarez-Borrego
- Departamento de Ecología Marina, at the Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Baja California, Mexico
| | - Robert L Brownell
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California
| | - Víctor Camacho-Ibar
- Instituto de Investigaciones Oceanológicas, at the Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Gerardo Ceballos
- Instituto Nacional de Ecología, at the Universidad Nacional Autónoma de México, Mexico City
| | | | | | - Philip A Hastings
- Scripps Institution of Oceanography, at the University of California, San Diego
| | - Gustavo Cárdenas-Hinojosa
- Departamento Biología de la Conservación, CICESE.,Instituto Nacional de Ecología y Cambio Climático, Ensenada
| | | | - Rodrigo Medellín
- Instituto Nacional de Ecología, at the Universidad Nacional Autónoma de México, Mexico City
| | - Sarah L Mesnick
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California
| | | | - Jorge Urbán
- Departamento de Ciencias Marinas y Costeras, at the Universidad Autónoma de Baja California Sur, La Paz, Mexico
| | - Enriqueta Velarde
- Instituto de Ciencias Marinas y Pesquerías, at the Universidad Veracruzana, Mexico
| | - Omar Vidal
- Desde lo Más Alto hasta lo Más Profundo, A.C., Mexico City
| | - Lloyd T Findley
- Centro de Investigación en Alimentación y Desarrollo (CIAD)-Unidad Guaymas, Sonora, Mexico
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California
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16
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Burgess MG, McDermott GR, Owashi B, Peavey Reeves LE, Clavelle T, Ovando D, Wallace BP, Lewison RL, Gaines SD, Costello C. Protecting marine mammals, turtles, and birds by rebuilding global fisheries. Science 2018; 359:1255-1258. [DOI: 10.1126/science.aao4248] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/26/2018] [Indexed: 11/02/2022]
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