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Tebbe J, Havenstein K, Forcada J, Tiedemann R, Caspers B, Hoffman JI. No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals. Proc Biol Sci 2024; 291:20232519. [PMID: 38503331 PMCID: PMC10950461 DOI: 10.1098/rspb.2023.2519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background. We addressed this issue in Antarctic fur seals by analysing skin swabs together with full-length MHC DQB II exon 2 sequences and data from 41 genome-wide distributed microsatellites. We did not find any effects of MHC relatedness on chemical similarity and there was also no relationship between MHC heterozygosity and chemical diversity. However, multilocus heterozygosity showed a significant positive association with chemical diversity, even after controlling for MHC heterozygosity. Our results appear to rule out a dominant role of the MHC in the chemical encoding of genetic information in a wild vertebrate population and highlight the need for genome-wide approaches to elucidate the mechanism(s) and specific genes underlying genotype-odour associations.
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Affiliation(s)
- Jonas Tebbe
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Department of Behavioural Ecology, Bielefeld University, 33501 Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
| | - Katja Havenstein
- Unit of Evolutionary Biology / Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Jaume Forcada
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Ralph Tiedemann
- Unit of Evolutionary Biology / Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Barbara Caspers
- Department of Behavioural Ecology, Bielefeld University, 33501 Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
| | - Joseph I. Hoffman
- Department of Evolutionary Population Genetics, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
- Department of Animal Behaviour, Bielefeld University, 33501 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Bielefeld, Germany
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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2
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Ouled-Cheikh J, March D, Borras-Chavez R, Drago M, Goebel ME, Fariña JM, Gazo M, Coll M, Cardona L. Future climate-induced distribution shifts in a sexually dimorphic key predator of the Southern Ocean. GLOBAL CHANGE BIOLOGY 2024; 30:e17191. [PMID: 38433338 DOI: 10.1111/gcb.17191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 03/05/2024]
Abstract
The response to climate change in highly dimorphic species can be hindered by differences between sexes in habitat preferences and movement patterns. The Antarctic fur seal, Arctocephalus gazella, is the most abundant pinniped in the Southern Hemisphere, and one of the main consumers of Antarctic krill, Euphausia superba, in the Southern Ocean. However, the populations breeding in the Atlantic Southern Ocean are decreasing, partly due to global warming. Male and female Antarctic fur seals differ greatly in body size and foraging ecology, and little is known about their sex-specific responses to climate change. We used satellite tracking data and Earth System Models to predict changes in habitat suitability for male and female Antarctic fur seals from the Western Antarctic Peninsula under different climate change scenarios. Under the most extreme scenario (SSP5-8.5; global average temperature +4.4°C projected by 2100), suitable habitat patches will shift southward during the non-breeding season, leading to a minor overall habitat loss. The impact will be more pronounced for females than for males. The reduction of winter foraging grounds might decrease the survival of post-weaned females, reducing recruitment and jeopardizing population viability. During the breeding season, when males fast on land, suitable foraging grounds for females off the South Shetland Islands will remain largely unmodified, and new ones will emerge in the Bellingshausen Sea. As Antarctic fur seals are income breeders, the foraging grounds of females should be reasonably close to the breeding colony. As a result, the new suitable foraging grounds will be useful for females only if nearby beaches currently covered by sea ice emerge by the end of the century. Furthermore, the colonization of these new, ice-free breeding locations might be limited by strong female philopatry. These results should be considered when managing the fisheries of Antarctic krill in the Southern Ocean.
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Affiliation(s)
- Jazel Ouled-Cheikh
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- iMARES group, Departament de Recursos Marins Renovables, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - David March
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, Paterna, València, Spain
- Centre for Ecology and Conservation, College of Life and Environmental Science, University of Exeter, Penryn, Cornwall, UK
| | - Renato Borras-Chavez
- Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Biology, Baylor University, Waco, Texas, USA
| | - Massimiliano Drago
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Michael E Goebel
- Institute of Marine Sciences, University of California Santa Cruz (UCSC), Santa Cruz, California, USA
- Antarctic Ecosystem Research Division, SWFSC, NMFS, NOAA, La Jolla, California, USA
| | - José M Fariña
- Center of Applied Ecology and Sustainability (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manel Gazo
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Marta Coll
- iMARES group, Departament de Recursos Marins Renovables, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
- Ecopath International Initiative (EII), Barcelona, Spain
| | - Luis Cardona
- Institut de Recerca de la Biodiversitat (IRBio) and Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals (BEECA), Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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3
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Forcada J, Hoffman JI, Gimenez O, Staniland IJ, Bucktrout P, Wood AG. Ninety years of change, from commercial extinction to recovery, range expansion and decline for Antarctic fur seals at South Georgia. GLOBAL CHANGE BIOLOGY 2023; 29:6867-6887. [PMID: 37839801 DOI: 10.1111/gcb.16947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023]
Abstract
With environmental change, understanding how species recover from overharvesting and maintain viable populations is central to ecosystem restoration. Here, we reconstruct 90 years of recovery trajectory of the Antarctic fur seal at South Georgia (S.W. Atlantic), a key indicator species in the krill-based food webs of the Southern Ocean. After being harvested to commercial extinction by 1907, this population rebounded and now constitutes the most abundant otariid in the World. However, its status remains uncertain due to insufficient and conflicting data, and anthropogenic pressures affecting Antarctic krill, an essential staple for millions of fur seals and other predators. Using integrated population models, we estimated simultaneously the long-term abundance for Bird Island, northwest South Georgia, epicentre of recovery of the species after sealing, and population adjustments for survey counts with spatiotemporal applicability. Applied to the latest comprehensive survey data, we estimated the population at South Georgia in 2007-2009 as 3,510,283 fur seals [95% CI: 3,140,548-3,919,604] (ca. 98% of global population), after 40 years of maximum growth and range expansion owing to an abundant krill supply. At Bird Island, after 50 years of exponential growth followed by 25 years of slow stable growth, the population collapsed in 2009 and has thereafter declined by -7.2% [-5.2, -9.1] per annum, to levels of the 1970s. For the instrumental record, this trajectory correlates with a time-varying relationship between coupled climate and sea surface temperature cycles associated with low regional krill availability, although the effects of increasing krill extraction by commercial fishing and natural competitors remain uncertain. Since 2015, fur seal longevity and recruitment have dropped, sexual maturation has retarded, and population growth is expected to remain mostly negative and highly variable. Our analysis documents the rise and fall of a key Southern Ocean predator over a century of profound environmental and ecosystem change.
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Affiliation(s)
- Jaume Forcada
- British Antarctic Survey, Natural Environment Research Council, UKRI, Cambridge, UK
| | - Joseph I Hoffman
- British Antarctic Survey, Natural Environment Research Council, UKRI, Cambridge, UK
- Department of Animal Behavior, University of Bielefeld, Bielefeld, Germany
| | - Olivier Gimenez
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | | | - Pete Bucktrout
- British Antarctic Survey, Natural Environment Research Council, UKRI, Cambridge, UK
| | - Andrew G Wood
- British Antarctic Survey, Natural Environment Research Council, UKRI, Cambridge, UK
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4
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Clark MS, Hoffman JI, Peck LS, Bargelloni L, Gande D, Havermans C, Meyer B, Patarnello T, Phillips T, Stoof-Leichsenring KR, Vendrami DLJ, Beck A, Collins G, Friedrich MW, Halanych KM, Masello JF, Nagel R, Norén K, Printzen C, Ruiz MB, Wohlrab S, Becker B, Dumack K, Ghaderiardakani F, Glaser K, Heesch S, Held C, John U, Karsten U, Kempf S, Lucassen M, Paijmans A, Schimani K, Wallberg A, Wunder LC, Mock T. Multi-omics for studying and understanding polar life. Nat Commun 2023; 14:7451. [PMID: 37978186 PMCID: PMC10656552 DOI: 10.1038/s41467-023-43209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Polar ecosystems are experiencing amongst the most rapid rates of regional warming on Earth. Here, we discuss 'omics' approaches to investigate polar biodiversity, including the current state of the art, future perspectives and recommendations. We propose a community road map to generate and more fully exploit multi-omics data from polar organisms. These data are needed for the comprehensive evaluation of polar biodiversity and to reveal how life evolved and adapted to permanently cold environments with extreme seasonality. We argue that concerted action is required to mitigate the impact of warming on polar ecosystems via conservation efforts, to sustainably manage these unique habitats and their ecosystem services, and for the sustainable bioprospecting of novel genes and compounds for societal gain.
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Affiliation(s)
- M S Clark
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - J I Hoffman
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany.
| | - L S Peck
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK.
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - D Gande
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - C Havermans
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - B Meyer
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Viale dell'Università 16, I-35020, Legnaro, Italy
| | - T Phillips
- British Antarctic Survey, UKRI-NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - K R Stoof-Leichsenring
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, 14473, Potsdam, Germany
| | - D L J Vendrami
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - A Beck
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München (SNSB-BSM), Menzinger Str. 67, 80638, München, Germany
| | - G Collins
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Manaaki Whenua-Landcare Research, 231 Morrin Road St Johns, Auckland, 1072, New Zealand
| | - M W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - K M Halanych
- Center for Marine Science, University of North Carolina, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - J F Masello
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- Justus-Liebig-Universität Gießen, Giessen, Germany
| | - R Nagel
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - K Norén
- Department of Zoology, Stockholm University, 106 91, Stockholm, Sweden
| | - C Printzen
- Senckenberg Biodiversity and Climate Research Centre & Loewe-Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
- Natural History Museum Frankfurt, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - M B Ruiz
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Universität Duisburg-Essen, Universitätstrasse 5, 45151, Essen, Germany
| | - S Wohlrab
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 23129, Oldenburg, Germany
| | - B Becker
- Universität zu Köln, Institut für Pflanzenwissenschaften, Zülpicher Str. 47b, 60674, Köln, Germany
| | - K Dumack
- Universität zu Köln, Terrestrische Ökologie, Zülpicher Str. 47b, 60674, Köln, Germany
| | - F Ghaderiardakani
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany
| | - K Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Heesch
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - C Held
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U John
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - U Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - S Kempf
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - M Lucassen
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - A Paijmans
- Universität Bielefeld, VHF, Konsequenz 45, 33615, Bielefeld, Germany
| | - K Schimani
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195, Berlin, Germany
| | - A Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - L C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry & MARUM, University of Bremen, Leobener Straße 3, 28359, Bremen, Germany
| | - T Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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Bender AN, Krause DJ, Goebel ME, Hoffman JI, Lewallen EA, Bonin CA. Genetic diversity and demographic history of the leopard seal: A Southern Ocean top predator. PLoS One 2023; 18:e0284640. [PMID: 37566609 PMCID: PMC10420386 DOI: 10.1371/journal.pone.0284640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/14/2023] [Indexed: 08/13/2023] Open
Abstract
Leopard seals (Hydrurga leptonyx) are top predators that can exert substantial top-down control of their Antarctic prey species. However, population trends and genetic diversity of leopard seals remain understudied, limiting our understanding of their ecological role. We investigated the genetic diversity, effective population size and demographic history of leopard seals to provide fundamental data that contextualizes their predatory influence on Antarctic ecosystems. Ninety leopard seals were sampled from the northern Antarctic Peninsula during the austral summers of 2008-2019 and a 405bp segment of the mitochondrial control region was sequenced for each individual. We uncovered moderate levels of nucleotide (π = 0.013) and haplotype (Hd = 0.96) diversity, and the effective population size was estimated at around 24,000 individuals (NE = 24,376; 95% CI: 16,876-33,126). Consistent with findings from other ice-breeding pinnipeds, Bayesian skyline analysis also revealed evidence for population expansion during the last glacial maximum, suggesting that historical population growth may have been boosted by an increase in the abundance of sea ice. Although leopard seals can be found in warmer, sub-Antarctic locations, the species' core habitat is centered on the Antarctic, making it inherently vulnerable to the loss of sea ice habitat due to climate change. Therefore, detailed assessments of past and present leopard seal population trends are needed to inform policies for Antarctic ecosystems.
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Affiliation(s)
- Arona N. Bender
- Marine and Environmental Sciences Department, Hampton University, Hampton, VA, United States of America
| | - Douglas J. Krause
- Antarctic Ecosystem Research Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, CA, United States of America
| | - Michael E. Goebel
- Ecology and Evolutionary Biology Department, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
- British Antarctic Survey, Cambridge, United Kingdom
| | - Eric A. Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
| | - Carolina A. Bonin
- Marine and Environmental Sciences Department, Hampton University, Hampton, VA, United States of America
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
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Hoffman JI, Heesch S, Clark MS. Editorial: Polar Genomics in a Changing World. Genes (Basel) 2023; 14:1395. [PMID: 37510300 PMCID: PMC10379204 DOI: 10.3390/genes14071395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Polar regions play critical roles in the function of the Earth's climate system, many of which are underpinned by their endemic biota [...].
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Affiliation(s)
- Joseph Ivan Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 10 01 31, 33615 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Svenja Heesch
- Applied Ecology & Phycology, Institute for Biosciences, University of Rostock, 18059 Rostock, Germany
| | - Melody Susan Clark
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
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7
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Salmerón N, Belle S, Cruz FS, Alegria N, Finger JVG, Corá DH, Petry MV, Hernández C, Cárdenas CA, Krüger L. Contrasting environmental conditions precluded lower availability of Antarctic krill affecting breeding chinstrap penguins in the Antarctic Peninsula. Sci Rep 2023; 13:5265. [PMID: 37002269 PMCID: PMC10066220 DOI: 10.1038/s41598-023-32352-7] [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: 09/13/2022] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
Dramatic decreases of chinstrap penguin populations across the Antarctic Peninsula (AP) are thought to be influenced by climate-driven changes affecting its main prey, the Antarctic krill, however, empirical evidence supporting such hypotheses are scarce. By coupling data on breeding chinstrap penguins, environmental remote sensing and estimates of krill acoustic density, we were able to demonstrate that penguins substantially increased their foraging effort in a year of low krill availability, with consequent reduction in breeding success. A winter of low sea ice cover followed by a summer/spring with stronger wind and lower marine productivity explained the lower and deeper krill availability. Our results highlight the importance of environmental variability on penguin populations, as variability is expected to increase under climate change, affecting foraging behaviour responses.
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Affiliation(s)
- Nuria Salmerón
- International Master of Science in Marine Biological Resources (IMBRSea), Ghent University, Krijgslaan 281/S8, Ghent, Belgium
| | - Solenne Belle
- International Master of Science in Marine Biological Resources (IMBRSea), Ghent University, Krijgslaan 281/S8, Ghent, Belgium
| | - Francisco Santa Cruz
- Departamento Científico, Instituto Antártico Chileno, Plaza Muñoz Gamero, 1055, Punta Arenas, Chile
| | - Nicolás Alegria
- Instituto de Investigación Pesquera (INPESCA), Colón, 2780, Talcahuano, Chile
| | - Júlia Victória Grohmann Finger
- Laboratório de Ornitologia e Animais Marinhos, Universidade do Vale do Rio dos Sinos (UNISINOS), Av. Unisinos, 950, São Leopoldo, Rio Grande do Sul, Brazil
| | - Denyelle Hennayra Corá
- Laboratório de Ornitologia e Animais Marinhos, Universidade do Vale do Rio dos Sinos (UNISINOS), Av. Unisinos, 950, São Leopoldo, Rio Grande do Sul, Brazil
| | - Maria Virginia Petry
- Laboratório de Ornitologia e Animais Marinhos, Universidade do Vale do Rio dos Sinos (UNISINOS), Av. Unisinos, 950, São Leopoldo, Rio Grande do Sul, Brazil
| | | | - César A Cárdenas
- Departamento Científico, Instituto Antártico Chileno, Plaza Muñoz Gamero, 1055, Punta Arenas, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras, 3425, Ñuñoa, Santiago, Chile
| | - Lucas Krüger
- Departamento Científico, Instituto Antártico Chileno, Plaza Muñoz Gamero, 1055, Punta Arenas, Chile.
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras, 3425, Ñuñoa, Santiago, Chile.
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8
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Yakupova A, Tomarovsky A, Totikov A, Beklemisheva V, Logacheva M, Perelman PL, Komissarov A, Dobrynin P, Krasheninnikova K, Tamazian G, Serdyukova NA, Rayko M, Bulyonkova T, Cherkasov N, Pylev V, Peterfeld V, Penin A, Balanovska E, Lapidus A, OBrien SJ, Graphodatsky A, Koepfli KP, Kliver S. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal. Genes (Basel) 2023; 14:genes14030619. [PMID: 36980891 PMCID: PMC10048373 DOI: 10.3390/genes14030619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/31/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial–interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3–0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.
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Affiliation(s)
- Aliya Yakupova
- Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia
- Correspondence: (A.Y.); (A.G.)
| | - Andrey Tomarovsky
- Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Azamat Totikov
- Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Violetta Beklemisheva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Maria Logacheva
- Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Polina L. Perelman
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Aleksey Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 9 Ulitsa Lomonosova, 191002 Saint Petersburg, Russia
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, 19701 Saint Petersburg, Russia
- Human Genetics Laboratory, Vavilov Institute of General Genetics RAS, 119991 Moscow, Russia
| | | | - Gaik Tamazian
- Centre for Computational Biology, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Natalia A. Serdyukova
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
| | - Mike Rayko
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Tatiana Bulyonkova
- Laboratory of Mixed Computations, A.P. Ershov Institute of Informatics Systems SB RAS, 630090 Novosibirsk, Russia
| | - Nikolay Cherkasov
- Centre for Computational Biology, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia
| | - Vladimir Pylev
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Vladimir Peterfeld
- Baikal Branch of State Research and Industrial Center of Fisheries, 670034 Ulan-Ude, Russia
| | - Aleksey Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia
| | - Elena Balanovska
- Laboratory of Human Population Genetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Alla Lapidus
- Center for Bioinformatics and Algorithmic Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - DNA Zoo Consortium
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen J. OBrien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, NOVA Southeastern University, Fort Lauderdale, FL 33004, USA
| | - Alexander Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia
- Correspondence: (A.Y.); (A.G.)
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, 1500 Remount Road, Front Royal, VA 22630, USA
- Center for Species Survival, Smithsonian’s National Zoo and Conservation Biology Institute, 1500 Remount Road, Front Royal, VA 22630, USA
| | - Sergei Kliver
- Center for Evolutionary Hologenomics, The Globe Institute, The University of Copenhagen, 5A, Oester Farimagsgade, 1353 Copenhagen, Denmark
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Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Sci Rep 2022; 12:17933. [PMID: 36289307 PMCID: PMC9606363 DOI: 10.1038/s41598-022-21658-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/29/2022] [Indexed: 01/20/2023] Open
Abstract
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
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