1
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Coombs EJ, Knapp A, Park T, Bennion RF, McCurry MR, Lanzetti A, Boessenecker RW, McGowen MR. Drivers of morphological evolution in the toothed whale jaw. Curr Biol 2024; 34:273-285.e3. [PMID: 38118449 DOI: 10.1016/j.cub.2023.11.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 12/22/2023]
Abstract
Toothed whales (odontocetes) emit high-frequency underwater sounds (echolocate)-an extreme and unique innovation allowing them to sense their prey and environment. Their highly specialized mandible (lower jaw) allows high-frequency sounds to be transmitted back to the inner ear. Echolocation is evident in the earliest toothed whales, but little research has focused on the evolution of mandibular form regarding this unique adaptation. Here, we use a high-density, three-dimensional geometric morphometric analysis of 100 living and extinct cetacean species spanning their ∼50-million-year evolutionary history. Our analyses demonstrate that most shape variation is found in the relative length of the jaw and the mandibular symphysis. The greatest morphological diversity was obtained during two periods of rapid evolution: the initial evolution of archaeocetes (stem whales) in the early to mid-Eocene as they adapted to an aquatic lifestyle, representing one of the most extreme adaptive transitions known, and later on in the mid-Oligocene odontocetes as they became increasingly specialized for a range of diets facilitated by increasingly refined echolocation. Low disparity in the posterior mandible suggests the shape of the acoustic window, which receives sound, has remained conservative since the advent of directional hearing in the aquatic archaeocetes, even as the earliest odontocetes began to receive sounds from echolocation. Diet, echolocation, feeding method, and dentition type strongly influence mandible shape. Unlike in the toothed whale cranium, we found no significant asymmetry in the mandible. We suggest that a combination of refined echolocation and associated dietary specializations have driven morphology and disparity in the toothed whale mandible.
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Affiliation(s)
- Ellen J Coombs
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St & Constitution Ave NW, Washington, DC 20560, USA; Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Andrew Knapp
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK; University College London, Gower Street, London WC1E 6BT, UK
| | - Travis Park
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK; School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Rebecca F Bennion
- Evolution & Diversity Dynamics Lab, Department of Geology, University of Liege, 4000 Liege, Belgium; O.D. Earth and History of Life, Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Matthew R McCurry
- Australian Museum Research Institute, 1 William Street, Sydney, NSW 2010, Australia; Earth & Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences (BEES), University of New South Wales, Kensington, NSW 2052, Australia; Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Agnese Lanzetti
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK; School of Geography, Earth, and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert W Boessenecker
- University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael R McGowen
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St & Constitution Ave NW, Washington, DC 20560, USA
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2
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Gillet A, Frédérich B, Pierce SE, Parmentier E. Iterative Habitat Transitions are Associated with Morphological Convergence of the Backbone in Delphinoids. J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09615-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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3
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Racicot R. Evolution of whale sensory ecology: Frontiers in nondestructive anatomical investigations. Anat Rec (Hoboken) 2021; 305:736-752. [PMID: 34546007 DOI: 10.1002/ar.24761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/09/2021] [Accepted: 07/14/2021] [Indexed: 12/18/2022]
Abstract
Studies surrounding the evolution of sensory system anatomy in cetaceans over the last ~100 years have shed light on aspects of the early evolution of hearing sensitivities, the small relative size of the organ of balance (semicircular canals and vestibule), brain (endocast) shape and relative volume changes, and ontogenetic development of sensory-related structures. Here, I review advances in our knowledge of sensory system anatomy as informed by the use of nondestructive imaging techniques, with a focus on applied methods in computed tomography (CT and μCT), and identify the key questions that remain to be addressed. Of these, the most important are: Is lower frequency hearing sensitivity the ancestral condition for whales? Did echolocation evolve more than once in odontocetes; and if so, when and why? How has the structure of the cetacean brain changed, through the evolution of whales, and does this correspond to changes in hearing sensitivities? Finally, what are the general pathways of ontogenetic development of sensory systems in odontocetes and mysticetes? Answering these questions will allow us to understand important macroevolutionary patterns in a fully aquatic mammalian group and provides baseline data on species for which we have limited biological information because of logistical limitations.
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Affiliation(s)
- Rachel Racicot
- Abteilung Messelforschung und Mammalogie, Senckenberg Forschungsinstitut und Naturkundemuseum, Frankfurt am Main, Germany.,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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4
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Morell M, IJsseldijk LL, Piscitelli-Doshkov M, Ostertag S, Estrade V, Haulena M, Doshkov P, Bourien J, Raverty SA, Siebert U, Puel JL, Shadwick RE. Cochlear apical morphology in toothed whales: Using the pairing hair cell-Deiters' cell as a marker to detect lesions. Anat Rec (Hoboken) 2021; 305:622-642. [PMID: 34096183 DOI: 10.1002/ar.24680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/17/2021] [Accepted: 04/15/2021] [Indexed: 11/06/2022]
Abstract
The apex or apical region of the cochlear spiral within the inner ear encodes for low-frequency sounds. The disposition of sensory hair cells on the organ of Corti is largely variable in the apical region of mammals, and it does not necessarily follow the typical three-row pattern of outer hair cells (OHCs). As most underwater noise sources contain low-frequency components, we expect to find most lesions in the apical region of the cochlea of toothed whales, in cases of permanent noise-induced hearing loss. To further understand how man-made noise might affect cetacean hearing, there is a need to describe normal morphological features of the apex and document interspecific anatomic variations in cetaceans. However, distinguishing between apical normal variability and hair cell death is challenging. We describe anatomical features of the organ of Corti of the apex in 23 ears from five species of toothed whales (harbor porpoise Phocoena phocoena, spinner dolphin Stenella longirostris, pantropical spotted dolphin Stenella attenuata, pygmy sperm whale Kogia breviceps, and beluga whale Delphinapterus leucas) by scanning electron microscopy and immunofluorescence. Our results showed an initial region where the lowest frequencies are encoded with two or three rows of OHCs, followed by the typical configuration of three OHC rows and three rows of supporting Deiters' cells. Whenever two rows of OHCs were detected, there were usually only two corresponding rows of supporting Deiters' cells, suggesting that the number of rows of Deiters' cells is a good indicator to distinguish between normal and pathological features.
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Affiliation(s)
- Maria Morell
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Büsum, Germany.,Institute for Neurosciences of Montpellier, University of Montpellier, INSERM Unit 1051, Montpellier, France.,Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lonneke L IJsseldijk
- Division of Pathology, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Sonja Ostertag
- School of Public Health, University of Waterloo, Waterloo, Ontario, Canada.,Freshwater Institute, Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | | | - Martin Haulena
- Vancouver Aquarium Marine Science Center, Vancouver, British Columbia, Canada
| | - Paul Doshkov
- Cape Hatteras National Seashore, Manteo, North Carolina, USA
| | - Jérôme Bourien
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM Unit 1051, Montpellier, France
| | - Stephen A Raverty
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada.,Animal Health Center, Animal Health Center, Ministry of Agriculture, Abbotsford, British Columbia, Canada
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Büsum, Germany
| | - Jean-Luc Puel
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM Unit 1051, Montpellier, France
| | - Robert E Shadwick
- Department of Zoology, The University of British Columbia, Vancouver, British Columbia, Canada
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5
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Groves SL, Peredo CM, Pyenson ND. What are the limits on whale ear bone size? Non-isometric scaling of the cetacean bulla. PeerJ 2021; 9:e10882. [PMID: 33604200 PMCID: PMC7869665 DOI: 10.7717/peerj.10882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/11/2021] [Indexed: 02/02/2023] Open
Abstract
The history of cetaceans demonstrates dramatic macroevolutionary changes that have aided their transformation from terrestrial to obligate aquatic mammals. Their fossil record shows extensive anatomical modifications that facilitate life in a marine environment. To better understand the constraints on this transition, we examined the physical dimensions of the bony auditory complex, in relation to body size, for both living and extinct cetaceans. We compared the dimensions of the tympanic bulla, a conch-shaped ear bone unique to cetaceans, with bizygomatic width—a proxy for cetacean body size. Our results demonstrate that cetacean ears scale non-isometrically with body size, with about 70% of variation explained by increases in bizygomatic width. Our results, which encompass the breadth of the whale fossil record, size diversity, and taxonomic distribution, suggest that functional auditory capacity is constrained by congruent factors related to cranial morphology, as opposed to allometrically scaling with body size.
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Affiliation(s)
- Sabrina L Groves
- Department of Paleobiology, National Museum of Natural History, Washington, DC, USA.,Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - Carlos Mauricio Peredo
- Department of Paleobiology, National Museum of Natural History, Washington, DC, USA.,Department of Earth and Environmental Science, University of Michigan - Ann Arbor, Ann Arbor, MI, USA.,Department of Marine Biology, Texas A&M University - Galveston, Galveston, TX, USA
| | - Nicholas 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
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6
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Ichishima H, Kawabe S, Sawamura H. The so-called foramen singulare in cetacean periotics is actually the superior vestibular area. Anat Rec (Hoboken) 2021; 304:1792-1799. [PMID: 33432669 DOI: 10.1002/ar.24585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/12/2020] [Accepted: 12/17/2020] [Indexed: 11/10/2022]
Abstract
It is nearly 100 years ago that the "foramen singulare" was first identified in cetacean periotics. Since then, the "foramen singulare" has been recognized in periotics of many cetacean species, extant or extinct. Surprisingly, however, it has never been confirmed if the foramen singulare in cetacean periotics is really homologous to that in other mammals. It is known that in mammals including humans the posterior ampullary nerve, which innervates the posterior semicircular duct, passes through the foramen singulare. We use an X-ray micro-CT scan to examine endocasts of the bony labyrinth of the inner ear of cetacean periotics, showing that the osseous canal extending from the so-called foramen singulare goes toward the anterior bony ampulla, meaning that the alleged foramen singulare in cetacean periotics is really the superior vestibular area, through which the utriculoampullary nerve enters. The transverse crest is quite significant to identify each quadrant of the fundus of the internal acoustic meatus, but in many cetacean species the transverse crest is poorly developed, almost imperceptible in some species, and this could have brought confusion into the interpretation over the superior vestibular area and the foramen singulare. The bony septum separating the cerebral aperture of the facial canal from the foramen singulare is not the transverse crest, but the perpendicular crest. The foramen singulare is not a distinct foramen separated from the inferior vestibular area. Instead, the true foramen singulare opens near the inferior vestibular area in the internal acoustic meatus in cetacean periotics.
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Affiliation(s)
| | - Soichiro Kawabe
- Institute of Dinosaur Research, Fukui Prefectural University, Eiheiji, Fukui, Japan
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7
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Martins MCI, Park T, Racicot R, Cooper N. Intraspecific variation in the cochleae of harbour porpoises (Phocoena phocoena) and its implications for comparative studies across odontocetes. PeerJ 2020; 8:e8916. [PMID: 32322439 PMCID: PMC7161573 DOI: 10.7717/peerj.8916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/15/2020] [Indexed: 12/19/2022] Open
Abstract
In morphological traits, variation within species is generally considered to be lower than variation among species, although this assumption is rarely tested. This is particularly important in fields like palaeontology, where it is common to use a single individual as representative of a species due to the rarity of fossils. Here, we investigated intraspecific variation in the cochleae of harbour porpoises (Phocoena phocoena). Interspecific variation of cochlear morphology is well characterised among odontocetes (toothed whales) because of the importance of the structure in echolocation, but generally these studies use only a single cochlea to represent each species. In this study we compare variation within the cochleae of 18 specimens of P. phocoena with variations in cochlear morphology across 51 other odontocete species. Using both 3D landmark and linear measurement data, we performed Generalised Procrustes and principal component analyses to quantify shape variation. We then quantified intraspecific variation in our sample of P. phocoena by estimating disparity and the coefficient of variation for our 3D and linear data respectively. Finally, to determine whether intraspecific variation may confound the results of studies of interspecific variation, we used multivariate and univariate analyses of variance to test whether variation within the specimens of P. phocoena was significantly lower than that across odontocetes. We found low levels of intraspecific variation in the cochleae of P. phocoena, and that cochlear shape within P. phocoena was significantly less variable than across odontocetes. Although future studies should attempt to use multiple cochleae for every species, our results suggest that using just one cochlea for each species should not strongly influence the conclusions of comparative studies if our results are consistent across Cetacea.
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Affiliation(s)
- Maria Clara Iruzun Martins
- Division of Biosciences, University College London, University of London, London, United Kingdom.,Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Travis Park
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Earth Sciences, University of Oxford, Oxford, United Kingdom
| | - Rachel Racicot
- Forschungsinstitut und Naturkundemuseum, Senckenberg der SNG, Frankfurt am Main, Germany.,The Dinosaur Institute, Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America.,Department of Earth and Environmental Sciences, Vanderbilt University, Nashville, TN, United States of America.,Department of Zoology, Smithsonian Museum of Natural History, Washington, DC, United States of America
| | - Natalie Cooper
- Department of Life Sciences, Natural History Museum, London, United Kingdom
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8
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Racicot RA, Boessenecker RW, Darroch SAF, Geisler JH. Evidence for convergent evolution of ultrasonic hearing in toothed whales (Cetacea: Odontoceti). Biol Lett 2019; 15:20190083. [PMID: 31088283 DOI: 10.1098/rsbl.2019.0083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Toothed whales (Cetacea: Odontoceti) are the most diverse group of modern cetaceans, originating during the Eocene/Oligocene transition approximately 38 Ma. All extant odontocetes echolocate; a single origin for this behaviour is supported by a unique facial source for ultrasonic vocalizations and a cochlea adapted for hearing the corresponding echoes. The craniofacial and inner ear morphology of Oligocene odontocetes support a rapid (less than 5 Myr) early evolution of echolocation. Although some cranial features in the stem odontocetes Simocetus and Olympicetus suggest an ability to generate ultrasonic sound, until now, the bony labyrinths of taxa of this grade have not been investigated. Here, we use µCT to examine a petrosal of a taxon with clear similarities to Olympicetus avitus. Measurements of the bony labyrinth, when added to an extensive dataset of cetartiodactyls, resulted in this specimen sharing a morphospace with stem whales, suggesting a transitional inner ear. This discovery implies that either the lineage leading to this Olympicetus--like taxon lost the ability to hear ultrasonic sound, or adaptations for ultrasonic hearing evolved twice, once in xenorophids and again on the stem of the odontocete crown group. We favour the latter interpretation as it matches a well-documented convergence of craniofacial morphology between xenorophids and extant odontocetes.
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Affiliation(s)
- Rachel A Racicot
- 1 W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, CA 91711 , USA.,2 Vertebrate Paleontology Department and The Dinosaur Institute, Natural History Museum of Los Angeles County , Los Angeles, CA 90007 , USA.,3 Department of Earth and Environmental Sciences, Vanderbilt University , Nashville, TN 37340 , USA
| | - Robert W Boessenecker
- 4 Department of Geology and Environmental Geosciences, College of Charleston , Charleston, SC 29414 , USA
| | - Simon A F Darroch
- 3 Department of Earth and Environmental Sciences, Vanderbilt University , Nashville, TN 37340 , USA
| | - Jonathan H Geisler
- 5 Department of Anatomy, New York Institute of Technology, College of Osteopathic Medicine , Old Westbury, NY 11568 , USA
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9
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Vasilopoulou-Kampitsi M, Goyens J, Van Damme R, Aerts P. The ecological signal on the shape of the lacertid vestibular system: simple versus complex microhabitats. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- M Vasilopoulou-Kampitsi
- Laboratory of Functional Morphology, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - J Goyens
- Laboratory of Functional Morphology, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - R Van Damme
- Laboratory of Functional Morphology, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - P Aerts
- Laboratory of Functional Morphology, Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
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10
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Galatius A, Olsen MT, Steeman ME, Racicot RA, Bradshaw CD, Kyhn LA, Miller LA. Raising your voice: evolution of narrow-band high-frequency signals in toothed whales (Odontoceti). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly194] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anders Galatius
- Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Morten Tange Olsen
- Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen O, Denmark
| | | | - Rachel A Racicot
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
- The Dinosaur Institute, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
- Department of Earth and Environmental Sciences, Vanderbilt University, Nashville, TN, USA
| | - Catherine D Bradshaw
- School of Geographical Sciences, University of Bristol, Bristol, UK
- Met Office Hadley Centre, Exeter, UK
| | - Line A Kyhn
- Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Lee A Miller
- Department of Biology, University of Southern Denmark, Odense, Denmark
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11
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Racicot RA, Darroch SAF, Kohno N. Neuroanatomy and inner ear labyrinths of the narwhal, Monodon monoceros, and beluga, Delphinapterus leucas (Cetacea: Monodontidae). J Anat 2018; 233:421-439. [PMID: 30033539 PMCID: PMC6131972 DOI: 10.1111/joa.12862] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2018] [Indexed: 10/28/2022] Open
Abstract
Narwhals (Monodon monoceros) and belugas (Delphinapterus leucas) are the only extant members of the Monodontidae, and are charismatic Arctic-endemic cetaceans that are at risk from global change. Investigating the anatomy and sensory apparatuses of these animals is essential to understanding their ecology and evolution, and informs efforts for their conservation. Here, we use X-ray CT scans to compare aspects of the endocranial and inner ear labyrinth anatomy of extant monodontids and use the overall morphology to draw larger inferences about the relationship between morphology and ecology. We show that differences in the shape of the brain, vasculature, and neural canals of both species may relate to differences in diving and other behaviors. The cochleae are similar in morphology in the two species, signifying similar hearing ranges and a close evolutionary relationship. Lastly, we compare two different methods for calculating 90var - a calculation independent of body size that is increasingly being used as a proxy for habitat preference. We show that a 'direct' angular measurement method shows significant differences between Arctic and other habitat preferences, but angle measurements based on planes through the semicircular canals do not, emphasizing the need for more detailed study and standardization of this measurement. This work represents the first comparative internal anatomical study of the endocranium and inner ear labyrinths of this small clade of toothed whales.
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Affiliation(s)
- Rachel A. Racicot
- Department of Earth and Environmental SciencesVanderbilt UniversityNashvilleTNUSA
- The Dinosaur InstituteNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Simon A. F. Darroch
- Department of Earth and Environmental SciencesVanderbilt UniversityNashvilleTNUSA
| | - Naoki Kohno
- Department of Geology and PaleontologyNational Museum of Nature and ScienceTokyoJapan
- Graduate School of Life and Environmental SciencesUniversity of TsukubaTsukubaJapan
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12
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Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
Abstract
The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.
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Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
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13
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The bony labyrinth of toothed whales reflects both phylogeny and habitat preferences. Sci Rep 2018; 8:7841. [PMID: 29777194 PMCID: PMC5959912 DOI: 10.1038/s41598-018-26094-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/20/2018] [Indexed: 11/08/2022] Open
Abstract
The inner ear of toothed whales (odontocetes) is known to have evolved particular shapes related to their abilities to echolocate and move under water. While the origin of these capacities is now more and more examined, thanks to new imaging techniques, little is still known about how informative inner ear shape could be to tackle phylogenetic issues or questions pertaining to the habitat preferences of extinct species. Here we show that the shape of the bony labyrinth of toothed whales provides key information both about phylogeny and habitat preferences (freshwater versus coastal and fully marine habitats). Our investigation of more than 20 species of extinct and modern odontocetes shows that the semi-circular canals are not very informative, in contrast to baleen whales, while the cochlea alone bears a strong signal. Inner ear shape thus provides a novel source of information to distinguish between morphologically convergent lineages (e.g. river dolphins).
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14
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Size Variation under Domestication: Conservatism in the inner ear shape of wolves, dogs and dingoes. Sci Rep 2017; 7:13330. [PMID: 29042574 PMCID: PMC5645459 DOI: 10.1038/s41598-017-13523-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022] Open
Abstract
A broad sample of wolves, dingoes, and domesticated dogs of different kinds and time periods was used to identify changes in size and shape of the organs of balance and hearing related to domestication and to evaluate the potential utility of uncovered patterns as markers of domestication. Using geometric morphometrics coupled with non-invasive imaging and three-dimensional reconstructions, we exposed and compared complex structures that remain largely conserved. There is no statistically significant difference in the levels of shape variation between prehistoric and modern dogs. Shape variance is slightly higher for the different components of the inner ear in modern dogs than in wolves, but these differences are not significant. Wolves express a significantly greater level of variance in the angle between the lateral and the posterior canal than domestic dog breeds. Wolves have smaller levels of size variation than dogs. In terms of the shape of the semicircular canals, dingoes reflect the mean shape in the context of variation in the sample. This mirrors the condition of feral forms in other organs, in which there is an incomplete return to the characteristics of the ancestor. In general, morphological diversity or disparity in the inner ear is generated by scaling.
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15
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Abstract
AbstractX-ray computed tomography (CT) provides a nondestructive means of studying the inside and outside of objects. It allows accurate visualization and measurement of internal features, that are otherwise impossible to obtain nondestructively, and is a lasting digital record that can be made available to future researchers, museums, and the general public. Here, an overview of CT scanning methodologies and protocol is provided, as well as some recent examples of how this technology is allowing paleontologists to make new inroads into understanding the ecology, evolution, and development of both extant and extinct organisms. Lastly, some frontiers and outstanding questions in the acquisition, processing, and storage of digital 3-D morphological data are highlighted.
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