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Suárez Menéndez M, Rivera-León VE, Robbins J, Berube M, Palsbøll PJ. PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms. PeerJ 2023; 11:e16028. [PMID: 37744223 PMCID: PMC10516101 DOI: 10.7717/peerj.16028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/13/2023] [Indexed: 09/26/2023] Open
Abstract
Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).
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Affiliation(s)
- Marcos Suárez Menéndez
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Vania E. Rivera-León
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Jooke Robbins
- Center for Coastal Studies, Provincetown, MA, United States of America
| | - Martine Berube
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Center for Coastal Studies, Provincetown, MA, United States of America
| | - Per J. Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Center for Coastal Studies, Provincetown, MA, United States of America
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Tangili M, Slettenhaar AJ, Sudyka J, Dugdale HL, Pen I, Palsbøll PJ, Verhulst S. DNA methylation markers of age(ing) in non-model animals. Mol Ecol 2023; 32:4725-4741. [PMID: 37401200 DOI: 10.1111/mec.17065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
Inferring the chronological and biological age of individuals is fundamental to population ecology and our understanding of ageing itself, its evolution, and the biological processes that affect or even cause ageing. Epigenetic clocks based on DNA methylation (DNAm) at specific CpG sites show a strong correlation with chronological age in humans, and discrepancies between inferred and actual chronological age predict morbidity and mortality. Recently, a growing number of epigenetic clocks have been developed in non-model animals and we here review these studies. We also conduct a meta-analysis to assess the effects of different aspects of experimental protocol on the performance of epigenetic clocks for non-model animals. Two measures of performance are usually reported, the R2 of the association between the predicted and chronological age, and the mean/median absolute deviation (MAD) of estimated age from chronological age, and we argue that only the MAD reflects accuracy. R2 for epigenetic clocks based on the HorvathMammalMethylChip4 was higher and the MAD scaled to age range lower, compared with other DNAm quantification approaches. Scaled MAD tended to be lower among individuals in captive populations, and decreased with an increasing number of CpG sites. We conclude that epigenetic clocks can predict chronological age with relatively high accuracy, suggesting great potential in ecological epigenetics. We discuss general aspects of epigenetic clocks in the hope of stimulating further DNAm-based research on ageing, and perhaps more importantly, other key traits.
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Affiliation(s)
- Marianthi Tangili
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Annabel J Slettenhaar
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joanna Sudyka
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, UK
| | - Ido Pen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Per J Palsbøll
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Center for Coastal Studies, Provincetown, Massachusetts, USA
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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Suárez-Menéndez M, Bérubé M, Furni F, Rivera-León VE, Heide-Jørgensen MP, Larsen F, Sears R, Ramp C, Eriksson BK, Etienne RS, Robbins J, Palsbøll PJ. Wild pedigrees inform mutation rates and historic abundance in baleen whales. Science 2023; 381:990-995. [PMID: 37651509 DOI: 10.1126/science.adf2160] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 07/25/2023] [Indexed: 09/02/2023]
Abstract
Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.
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Affiliation(s)
- Marcos Suárez-Menéndez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Martine Bérubé
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Center for Coastal Studies, Provincetown, MA, USA
| | - Fabrício Furni
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Vania E Rivera-León
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Finn Larsen
- National Institute of Aquatic Resources, Kongens Lyngby, Denmark
| | - Richard Sears
- Mingan Island Cetacean Study Inc., St. Lambert, Quebec, Canada
| | - Christian Ramp
- Mingan Island Cetacean Study Inc., St. Lambert, Quebec, Canada
- Scottish Oceans Institute, University of St. Andrews, St. Andrews, UK
| | - Britas Klemens Eriksson
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Per J Palsbøll
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Center for Coastal Studies, Provincetown, MA, USA
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de Kock W, Mackie M, Ramsøe M, Allentoft ME, Broderick AC, Haywood JC, Godley BJ, Snape RTE, Bradshaw PJ, Genz H, von Tersch M, Dee MW, Palsbøll PJ, Alexander M, Taurozzi AJ, Çakırlar C. Threatened North African seagrass meadows have supported green turtle populations for millennia. Proc Natl Acad Sci U S A 2023; 120:e2220747120. [PMID: 37459551 PMCID: PMC10372671 DOI: 10.1073/pnas.2220747120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/25/2023] [Indexed: 07/20/2023] Open
Abstract
"Protect and restore ecosystems and biodiversity" is the second official aim of the current UN Ocean Decade (2021 to 2030) calling for the identification and protection of critical marine habitats. However, data to inform policy are often lacking altogether or confined to recent times, preventing the establishment of long-term baselines. The unique insights gained from combining bioarchaeology (palaeoproteomics, stable isotope analysis) with contemporary data (from satellite tracking) identified habitats which sea turtles have been using in the Eastern Mediterranean over five millennia. Specifically, our analysis of archaeological green turtle (Chelonia mydas) bones revealed that they likely foraged on the same North African seagrass meadows as their modern-day counterparts. Here, millennia-long foraging habitat fidelity has been directly demonstrated, highlighting the significance (and long-term dividends) of protecting these critical coastal habitats that are especially vulnerable to global warming. We highlight the potential for historical ecology to inform policy in safeguarding critical marine habitats.
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Affiliation(s)
- Willemien de Kock
- Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, 9712ERGroningen, Netherlands
- Marine Evolution and Conservation Group, Groningen Institute for Evolutionary Life Sciences, Faculty of Science and Engineering, University of Groningen, 9747AGGroningen, Netherlands
| | - Meaghan Mackie
- The Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, 1353Copenhagen K, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Science, University of Copenhagen, 2200Copenhagen K, Denmark
| | - Max Ramsøe
- The Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, 1353Copenhagen K, Denmark
| | - Morten E. Allentoft
- Trace and Environmental DNA Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia6102, Australia
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1353Copenhagen K, Denmark
| | - Annette C. Broderick
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
| | - Julia C. Haywood
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
| | - Brendan J. Godley
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
| | - Robin T. E. Snape
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
- Society for the Protection of Turtles, Nicosia99150, North Cyprus
| | - Phil J. Bradshaw
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn Campus, PenrynTR10 9FE, United Kingdom
| | - Hermann Genz
- Department of History and Archaeology, American University of Beirut, Beirut1107 2020, Lebanon
| | - Matthew von Tersch
- BioArCh, Department of Archaeology, University of York, YorkYO10 5NG, United Kingdom
| | - Michael W. Dee
- Centre for Isotope Research, Faculty of Science and Engineering, University of Groningen, 9747AGGroningen, Netherlands
| | - Per J. Palsbøll
- Marine Evolution and Conservation Group, Groningen Institute for Evolutionary Life Sciences, Faculty of Science and Engineering, University of Groningen, 9747AGGroningen, Netherlands
- Center for Coastal Studies, Provincetown, MA02657
| | - Michelle Alexander
- BioArCh, Department of Archaeology, University of York, YorkYO10 5NG, United Kingdom
| | - Alberto J. Taurozzi
- The Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, 1353Copenhagen K, Denmark
| | - Canan Çakırlar
- Groningen Institute of Archaeology, Faculty of Arts, University of Groningen, 9712ERGroningen, Netherlands
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5
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Derville S, Torres LG, Newsome SD, Somes CJ, Valenzuela LO, Vander Zanden HB, Baker CS, Bérubé M, Busquets-Vass G, Carlyon K, Childerhouse SJ, Constantine R, Dunshea G, Flores PAC, Goldsworthy SD, Graham B, Groch K, Gröcke DR, Harcourt R, Hindell MA, Hulva P, Jackson JA, Kennedy AS, Lundquist D, Mackay AI, Neveceralova P, Oliveira L, Ott PH, Palsbøll PJ, Patenaude NJ, Rowntree V, Sironi M, Vermeuelen E, Watson M, Zerbini AN, Carroll EL. Long-term stability in the circumpolar foraging range of a Southern Ocean predator between the eras of whaling and rapid climate change. Proc Natl Acad Sci U S A 2023; 120:e2214035120. [PMID: 36848574 PMCID: PMC10013836 DOI: 10.1073/pnas.2214035120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/19/2022] [Indexed: 03/01/2023] Open
Abstract
Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis), that forages on copepods and krill from ~30°S to the Antarctic ice edge (>60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (>60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.
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Affiliation(s)
- Solène Derville
- Marine Mammal Institute, Oregon State University, Newport, OR97365
- Unité Mixte de Recherche (UMR) Entropie, French Institute of Research for Sustainable Development, Nouméa98848, New Caledonia
| | - Leigh G. Torres
- Marine Mammal Institute, Oregon State University, Newport, OR97365
| | - Seth D. Newsome
- Biology Department, University of New Mexico, Albuquerque, NM87131-0001
| | | | - Luciano O. Valenzuela
- Consejo Nacional de Investigaciones Científicas y Técnicas, Laboratorio de Ecología Evolutiva Humana, Facultad de Ciencias Sociales de la Universidad Nacional del Centro de la Provincia de Buenos Aires (FACSO-UNCPBA), 7631Buenos Aires, Argentina
- Instituto de Conservación de Ballenas, Ing. Maschwitz, 1623 Buenos Aires, Argentina
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112-0840
| | | | - C. Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, OR97365
- Department of Fisheries, Wildlife and Conservation Sciences, Oregon State University, Corvallis, OR97365
| | - Martine Bérubé
- Marine Evolution and Conservation Group, Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9747 AGGroningen, The Netherlands
- Centre for Coastal Studies, Provincetown, MA02657
| | - Geraldine Busquets-Vass
- Biology Department, University of New Mexico, Albuquerque, NM87131-0001
- Laboratorio de Macroecología Marina, Centro de Investigación Científica y Educación Superior de Ensenada, Unidad La Paz, 23050La Paz, BCS, México
| | - Kris Carlyon
- Department of Natural Resources and Environment Tasmania, Hobart7001, Australia
| | | | - Rochelle Constantine
- School of Biological Sciences, University of Auckland Waipapa Taumata Rau, Auckland1010, AotearoaNew Zealand
| | - Glenn Dunshea
- Ecological Marine Services Pty. Ltd., Bundaberg4670, QLD, Australia
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491Trondheim, Norway
| | - Paulo A. C. Flores
- Núcleo de Gestão Integrada ICMBio Florianópolis, Instituto Chico Mendes de Conservação da Biodiversidade, Ministério do Meio Ambiente, Florianópolis88053-700, Brazil
| | - Simon D. Goldsworthy
- South Australian Research and Development Institute, Primary Industries and Regions South Australia, Adelaide, SA5064, Australia
- School of Earth and Environmental Sciences University of Adelaide, Adelaide, SA5064, Australia
| | - Brittany Graham
- Environmental Law Initiative, Wellington6011, AotearoaNew Zealand
| | - Karina Groch
- Instituto Australis, Imbituba, SC88780-000, Brazil
| | - Darren R. Gröcke
- Stable Isotope Biogeochemistry Laboratory, Department of Earth Sciences, Durham University, DurhamDH1 3LE, United Kingdom
| | - Robert Harcourt
- School of Natural Sciences, Macquarie University, Sydney, NSW2000, Australia
| | - Mark A. Hindell
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7005, Australia
| | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University, Prague116 36, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava701 03, Czech Republic
| | | | - Amy S. Kennedy
- Cooperative Institute for Climate, Ecosystem and Ocean Studies, University of Washington & Marine Mammal Laboratory, Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), Seattle, WA98112
| | - David Lundquist
- New Zealand Department of Conservation - Te Papa Atawhai, Wellington6011, AotearoaNew Zealand
| | - Alice I. Mackay
- South Australian Research and Development Institute, Primary Industries and Regions South Australia, Adelaide, SA5064, Australia
| | - Petra Neveceralova
- Department of Zoology, Faculty of Science, Charles University, Prague116 36, Czech Republic
- Ivanhoe Sea Safaris, Gansbaai7220, South Africa
- Dyer Island Conservation Trust, Great White House, Kleinbaai, Van Dyks Bay7220, South Africa
| | - Larissa Oliveira
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, Torres, RS95560-000, Brazil
- Laboratório de Ecologia de Mamίferos, Universidade do Vale do Rio dos Sinos, Sao Leopoldo, RS93022-750, Brazil
| | - Paulo H. Ott
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, Torres, RS95560-000, Brazil
- Universidade Estadual do Rio Grande do Sul, Osório, RS95520-000, Brazil
| | - Per J. Palsbøll
- Marine Evolution and Conservation Group, Groningen Institute of Evolutionary Life Sciences, University of Groningen, 9747 AGGroningen, The Netherlands
- Centre for Coastal Studies, Provincetown, MA02657
| | | | - Victoria Rowntree
- Instituto de Conservación de Ballenas, Ing. Maschwitz, 1623 Buenos Aires, Argentina
- School of Biological Sciences, University of Utah, Salt Lake City, UT84112-0840
- Ocean Alliance, Gloucester, MA01930
| | - Mariano Sironi
- Instituto de Conservación de Ballenas, Ing. Maschwitz, 1623 Buenos Aires, Argentina
- Diversidad Biológica IV, Universidad Nacional de Córdoba, CórdobaX5000HUA, Argentina
| | - Els Vermeuelen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria0002, South Africa
| | - Mandy Watson
- Department of Environment, Land, Water and Planning, Warrnambool, VIC3280, Australia
| | - Alexandre N. Zerbini
- Cooperative Institute for Climate, Ecosystem and Ocean Studies, University of Washington & Marine Mammal Laboratory, Alaska Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), Seattle, WA98112
- Marine Ecology and Telemetry Research & Cascadia Research Collective, Seabeck, WA98380
| | - Emma L. Carroll
- School of Biological Sciences, University of Auckland Waipapa Taumata Rau, Auckland1010, AotearoaNew Zealand
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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7
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Christianen MJA, Smulders FOH, Vonk JA, Becking LE, Bouma TJ, Engel SM, James RK, Nava MI, de Smit JC, van der Zee JP, Palsbøll PJ, Bakker ES. Seagrass ecosystem multifunctionality under the rise of a flagship marine megaherbivore. Glob Chang Biol 2023; 29:215-230. [PMID: 36330798 PMCID: PMC10099877 DOI: 10.1111/gcb.16464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/09/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Large grazers (megaherbivores) have a profound impact on ecosystem functioning. However, how ecosystem multifunctionality is affected by changes in megaherbivore populations remains poorly understood. Understanding the total impact on ecosystem multifunctionality requires an integrative ecosystem approach, which is especially challenging to obtain in marine systems. We assessed the effects of experimentally simulated grazing intensity scenarios on ecosystem functions and multifunctionality in a tropical Caribbean seagrass ecosystem. As a model, we selected a key marine megaherbivore, the green turtle, whose ecological role is rapidly unfolding in numerous foraging areas where populations are recovering through conservation after centuries of decline, with an increase in recorded overgrazing episodes. To quantify the effects, we employed a novel integrated index of seagrass ecosystem multifunctionality based upon multiple, well-recognized measures of seagrass ecosystem functions that reflect ecosystem services. Experiments revealed that intermediate turtle grazing resulted in the highest rates of nutrient cycling and carbon storage, while sediment stabilization, decomposition rates, epifauna richness, and fish biomass are highest in the absence of turtle grazing. In contrast, intense grazing resulted in disproportionally large effects on ecosystem functions and a collapse of multifunctionality. These results imply that (i) the return of a megaherbivore can exert strong effects on coastal ecosystem functions and multifunctionality, (ii) conservation efforts that are skewed toward megaherbivores, but ignore their key drivers like predators or habitat, will likely result in overgrazing-induced loss of multifunctionality, and (iii) the multifunctionality index shows great potential as a quantitative tool to assess ecosystem performance. Considerable and rapid alterations in megaherbivore abundance (both through extinction and conservation) cause an imbalance in ecosystem functioning and substantially alter or even compromise ecosystem services that help to negate global change effects. An integrative ecosystem approach in environmental management is urgently required to protect and enhance ecosystem multifunctionality.
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Affiliation(s)
- Marjolijn J. A. Christianen
- Aquatic Ecology and Water Quality Management GroupWageningen University & ResearchWageningenThe Netherlands
- Marine Evolution and Conservation GroupGroningen Institute for Evolutionary Life Sciences, University of GroningenGroningenThe Netherlands
| | - Fee O. H. Smulders
- Aquatic Ecology and Water Quality Management GroupWageningen University & ResearchWageningenThe Netherlands
| | - Jan Arie Vonk
- Department of Freshwater and Marine EcologyInstitute for Biodiversity and Ecosystem Dynamics (IBED), University of AmsterdamAmsterdamThe Netherlands
| | - Leontine E. Becking
- Aquaculture and Fisheries groupWageningen University & Research CentreWageningenThe Netherlands
| | - Tjeerd J. Bouma
- Department of Estuarine and Delta Systems, Royal Netherlands Institute for Sea Research (NIOZ)YersekeThe Netherlands
- Department of Physical Geography, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Sabine M. Engel
- STINAPA, Bonaire National Parks FoundationBonaireCaribbean Netherlands
| | - Rebecca K. James
- Department of Estuarine and Delta Systems, Royal Netherlands Institute for Sea Research (NIOZ)YersekeThe Netherlands
- Biogeochemistry and Modeling of the Earth System GroupUniversité libre de BruxellesBruxellesBelgium
| | - Mabel I. Nava
- Sea Turtle Conservation BonaireBonaireCaribbean Netherlands
| | - Jaco C. de Smit
- Department of Estuarine and Delta Systems, Royal Netherlands Institute for Sea Research (NIOZ)YersekeThe Netherlands
- Department of Physical Geography, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Jurjan P. van der Zee
- Marine Evolution and Conservation GroupGroningen Institute for Evolutionary Life Sciences, University of GroningenGroningenThe Netherlands
| | - Per J. Palsbøll
- Marine Evolution and Conservation GroupGroningen Institute for Evolutionary Life Sciences, University of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Elisabeth S. Bakker
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Wildlife Ecology and Conservation Group, Wageningen University & ResearchWageningenThe Netherlands
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8
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Cabrera AA, Schall E, Bérubé M, Anderwald P, Bachmann L, Berrow S, Best PB, Clapham PJ, Cunha H, Dalla Rosa L, Dias C, Findlay K, Haug T, Heide‐Jørgensen MP, Hoelzel A, Kovacs KM, Landry S, Larsen F, Lopes XM, Lydersen C, Mattila DK, Oosting T, Pace RM, Papetti C, Paspati A, Pastene LA, Prieto R, Ramp C, Robbins J, Sears R, Secchi ER, Silva MA, Simon M, Víkingsson G, Wiig Ø, Øien N, Palsbøll PJ. Strong and lasting impacts of past global warming on baleen whales and their prey. Glob Chang Biol 2022; 28:2657-2677. [PMID: 35106859 PMCID: PMC9305191 DOI: 10.1111/gcb.16085] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 05/14/2023]
Abstract
Global warming is affecting the population dynamics and trophic interactions across a wide range of ecosystems and habitats. Translating these real-time effects into their long-term consequences remains a challenge. The rapid and extreme warming period that occurred after the Last Glacial Maximum (LGM) during the Pleistocene-Holocene transition (7-12 thousand years ago) provides an opportunity to gain insights into the long-term responses of natural populations to periods with global warming. The effects of this post-LGM warming period have been assessed in many terrestrial taxa, whereas insights into the impacts of rapid global warming on marine taxa remain limited, especially for megafauna. In order to understand how large-scale climate fluctuations during the post-LGM affected baleen whales and their prey, we conducted an extensive, large-scale analysis of the long-term effects of the post-LGM warming on abundance and inter-ocean connectivity in eight baleen whale and seven prey (fish and invertebrates) species across the Southern and the North Atlantic Ocean; two ocean basins that differ in key oceanographic features. The analysis was based upon 7032 mitochondrial DNA sequences as well as genome-wide DNA sequence variation in 100 individuals. The estimated temporal changes in genetic diversity during the last 30,000 years indicated that most baleen whale populations underwent post-LGM expansions in both ocean basins. The increase in baleen whale abundance during the Holocene was associated with simultaneous changes in their prey and climate. Highly correlated, synchronized and exponential increases in abundance in both baleen whales and their prey in the Southern Ocean were indicative of a dramatic increase in ocean productivity. In contrast, the demographic fluctuations observed in baleen whales and their prey in the North Atlantic Ocean were subtle, varying across taxa and time. Perhaps most important was the observation that the ocean-wide expansions and decreases in abundance that were initiated by the post-LGM global warming, continued for millennia after global temperatures stabilized, reflecting persistent, long-lasting impacts of global warming on marine fauna.
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Affiliation(s)
- Andrea A. Cabrera
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Elena Schall
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Martine Bérubé
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Pia Anderwald
- Swiss National ParkChastè Planta‐WildenbergZernezSwitzerland
| | | | - Simon Berrow
- Marine and Freshwater Research CentreGalway‐Mayo Institute of TechnologyGalwayIreland
- Irish Whale and Dolphin GroupMerchants QuayKilrushCounty ClareIreland
| | - Peter B. Best
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaHatfieldSouth Africa
| | | | - Haydée A. Cunha
- Aquatic Mammals and Bioindicators Laboratory (MAQUA)Faculty of OceanographyState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
- Genetics Department of the Biology InstituteState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
| | - Luciano Dalla Rosa
- Laboratory of Ecology and Conservation of Marine MegafaunaInstitute of OceanographyFederal University of Rio Grande‐FURGRio GrandeRio Grande do SulBrazil
| | - Carolina Dias
- Aquatic Mammals and Bioindicators Laboratory (MAQUA)Faculty of OceanographyState University of Rio de Janeiro ‐ UERJMaracanãRio de JaneiroBrazil
| | - Kenneth P. Findlay
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaHatfieldSouth Africa
- Department Conservation and Marine SciencesCentre for Sustainable Oceans EconomyCape Peninsula University of TechnologyCape TownSouth Africa
| | - Tore Haug
- Research Group Marine MammalsInstitute of Marine ResearchTromsøNorway
| | | | | | | | - Scott Landry
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Finn Larsen
- Section for Ecosystem based Marine ManagementNational Institute of Aquatic ResourcesTechnical University of DenmarkKongens LyngbyDenmark
| | - Xênia M. Lopes
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | | | | | - Tom Oosting
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Richard M. Pace
- Northeast Fisheries Science CenterNational Marine Fisheries ServiceWoods HoleMassachusettsUSA
| | | | - Angeliki Paspati
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Hellenic Agricultural Organisation‐“DIMITRA”HerakleionCreteGreece
| | | | - Rui Prieto
- Institute of Marine Sciences – Okeanos & Institute of Marine Research ‐ IMARUniversity of the AzoresHortaPortugal
| | - Christian Ramp
- Sea Mammal Research UnitScottish Oceans InstituteUniversity of St. AndrewsScotlandUK
- Mingan Island Cetacean StudySaint LambertQuébecCanada
| | - Jooke Robbins
- Center for Coastal StudiesProvincetownMassachusettsUSA
| | - Richard Sears
- Greenland Climate Research CentreGreenland Institute of Natural ResourcesNuukGreenland
| | - Eduardo R. Secchi
- Laboratory of Ecology and Conservation of Marine MegafaunaInstitute of OceanographyFederal University of Rio Grande‐FURGRio GrandeRio Grande do SulBrazil
| | - Mónica A. Silva
- Institute of Marine Sciences – Okeanos & Institute of Marine Research ‐ IMARUniversity of the AzoresHortaPortugal
| | - Malene Simon
- Greenland Climate Research CentreGreenland Institute of Natural ResourcesNuukGreenland
| | | | - Øystein Wiig
- Natural History MuseumUniversity of OsloOsloNorway
| | - Nils Øien
- Marine Mammal DivisionInstitute of Marine ResearchBergenNorway
| | - Per J. Palsbøll
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusettsUSA
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9
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Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M. The era of reference genomes in conservation genomics. Trends Ecol Evol 2022; 37:197-202. [PMID: 35086739 DOI: 10.1016/j.tree.2021.11.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 02/08/2023]
Abstract
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
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Affiliation(s)
- Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; University of Koblenz-Landau, Institute for Environmental Sciences, Fortstrasse 7, 76829 Landau, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Iliana Bista
- University of Cambridge, Department of Genetics, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, CB10 1SA, Hinxton, UK
| | | | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino (FI) 50019, Italy
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
| | - José A Godoy
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain
| | - Jacob Höglund
- Dept. of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Sweden
| | | | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Belgium
| | - Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences University of Groningen Nijenborgh, 9747, AG, Groningen, the Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5, 220 Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas, Av. Américo Vespucio, 26, 41092, Spain
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Belgium
| | | | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Dept. of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Germany
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark, Build 3, Universitetsparken 15, Copenhagen 2100, Denmark; China National Genebank, BGI-Shenzhen, Jinsha Road, Dapeng District, Shenzhen 518083, China
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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10
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van der Zee JP, Christianen MJA, Bérubé M, Nava M, van der Wal S, Berkel J, Bervoets T, Meijer Zu Schlochtern M, Becking LE, Palsbøll PJ. Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability. Mol Ecol 2021; 31:1044-1056. [PMID: 34861074 PMCID: PMC9299637 DOI: 10.1111/mec.16302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022]
Abstract
Pleistocene environmental changes are generally assumed to have dramatically affected species’ demography via changes in habitat availability, but this is challenging to investigate due to our limited knowledge of how Pleistocene ecosystems changed through time. Here, we tracked changes in shallow marine habitat availability resulting from Pleistocene sea level fluctuations throughout the last glacial cycle (120–14 thousand years ago; kya) and assessed correlations with past changes in genetic diversity inferred from genome‐wide SNPs, obtained via ddRAD sequencing, in Caribbean hawksbill turtles, which feed in coral reefs commonly found in shallow tropical waters. We found sea level regression resulted in an average 75% reduction in shallow marine habitat availability during the last glacial cycle. Changes in shallow marine habitat availability correlated strongly with past changes in hawksbill turtle genetic diversity, which gradually declined to ~1/4th of present‐day levels during the Last Glacial Maximum (LGM; 26–19 kya). Shallow marine habitat availability and genetic diversity rapidly increased after the LGM, signifying a population expansion in response to warming environmental conditions. Our results suggest a positive correlation between Pleistocene environmental changes, habitat availability and species’ demography, and that demographic changes in hawksbill turtles were potentially driven by feeding habitat availability. However, we also identified challenges associated with disentangling the potential environmental drivers of past demographic changes, which highlights the need for integrative approaches. Our conclusions underline the role of habitat availability on species’ demography and biodiversity, and that the consequences of ongoing habitat loss should not be underestimated.
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Affiliation(s)
- Jurjan P van der Zee
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Wageningen Marine Research, Den Helder, the Netherlands
| | - Marjolijn J A Christianen
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Martine Bérubé
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Center for Coastal Studies, Provincetown, Massachusetts, USA
| | - Mabel Nava
- Sea Turtle Conservation Bonaire, Kralendijk, Bonaire, Caribbean Netherlands
| | | | - Jessica Berkel
- Sint Eustatius National Parks Foundation, Sint Eustatius, Caribbean Netherlands
| | - Tadzio Bervoets
- Sint Maarten Nature Foundation, Cole Bay, Sint Maarten.,Dutch Caribbean Nature Alliance, Kralendijk, Bonaire, Caribbean Netherlands
| | | | - Leontine E Becking
- Wageningen Marine Research, Den Helder, the Netherlands.,Marine Animal Ecology Group, Wageningen University & Research, Wageningen, the Netherlands
| | - Per J Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, AG Groningen, the Netherlands.,Center for Coastal Studies, Provincetown, Massachusetts, USA
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11
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van den Berg GL, Vermeulen E, Valenzuela LO, Bérubé M, Ganswindt A, Gröcke DR, Hall G, Hulva P, Neveceralova P, Palsbøll PJ, Carroll EL. Decadal shift in foraging strategy of a migratory southern ocean predator. Glob Chang Biol 2020; 27:1052-1067. [PMID: 33319502 DOI: 10.1111/gcb.15465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Rapid anthropogenic environmental change is expected to impact a host of ecological parameters in Southern Ocean ecosystems. Of critical concern are the consequences of these changes on the range of species that show fidelity to migratory destinations, as philopatry is hypothesized to help or hinder adaptation to climate change depending on the circumstances. Many baleen whales show philopatry to feeding grounds and are also capital breeders that meet migratory and reproductive costs through seasonal energy intake. Southern right whales (Eubalaena australis, SRWs) are capital breeders that have a strong relationship between reproductive output and foraging success. The population dynamics of South Africa's population of SRWs are characterized by two distinct periods: the 1990s, a period of high calving rates; and the late 2010s, a period associated with lowered calving rates. Here we use analyses of stable carbon (δ13 C) and nitrogen (δ15 N) isotope values from SRW biopsy samples (n = 122) collected during these two distinct periods to investigate foraging ecology of the South African population of SRWs over a time period coincident with the demographic shift. We show that South African SRWs underwent a dramatic northward shift, and diversification, in foraging strategy from 1990s to 2010s. Bayesian mixing model results suggest that during the 1990s, South African SRWs foraged on prey isotopically similar to South Georgia/Islas Georgias del Sur krill. In contrast, in the 2010s, South African SRWs foraged on prey isotopically consistent with the waters of the Subtropical Convergence, Polar Front and Marion Island. We hypothesize that this shift represents a response to changes in preferred habitat or prey, for example, the decrease in abundance and southward range contraction of Antarctic krill. By linking reproductive decline to changing foraging strategies for the first time in SRWs, we show that altering foraging strategies may not be sufficient to adapt to a changing ocean.
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Affiliation(s)
- Gideon L van den Berg
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Els Vermeulen
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Luciano O Valenzuela
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Ecología Evolutiva Humana (LEEH, Facultad de Ciencias Sociales, Unidad de Enseñanza Universitaria Quequén, UNCPBA, Buenos Aires, Argentina
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
- Instituto de Conservación de Ballenas, Buenos Aires, Argentina
| | - Martine Bérubé
- Marine Evolution and Conservation Group, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Centre for Coastal Studies, Provincetown, MA, USA
| | - Andre Ganswindt
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Darren R Gröcke
- Stable Isotope Biogeochemistry Laboratory (SIBL), Department of Earth Sciences, Durham University, Durham, UK
| | - Grant Hall
- Department of Zoology and Entomology, Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petra Neveceralova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Ivanhoe Sea Safaris, Gansbaai, South Africa
- Dyer Island Conservation Trust, Great White House, Kleinbaai, South Africa
| | - Per J Palsbøll
- Marine Evolution and Conservation Group, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Centre for Coastal Studies, Provincetown, MA, USA
| | - Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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12
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van der Zee JP, Christianen MJA, Nava M, Velez-Zuazo X, Hao W, Bérubé M, van Lavieren H, Hiwat M, Berzins R, Chevalier J, Chevallier D, Lankester MC, Bjorndal KA, Bolten AB, Becking LE, Palsbøll PJ. Population recovery changes population composition at a major southern Caribbean juvenile developmental habitat for the green turtle, Chelonia mydas. Sci Rep 2019; 9:14392. [PMID: 31591419 PMCID: PMC6779738 DOI: 10.1038/s41598-019-50753-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/18/2019] [Indexed: 11/09/2022] Open
Abstract
Understanding the population composition and dynamics of migratory megafauna at key developmental habitats is critical for conservation and management. The present study investigated whether differential recovery of Caribbean green turtle (Chelonia mydas) rookeries influenced population composition at a major juvenile feeding ground in the southern Caribbean (Lac Bay, Bonaire, Caribbean Netherlands) using genetic and demographic analyses. Genetic divergence indicated a strong temporal shift in population composition between 2006-2007 and 2015-2016 (ϕST = 0.101, P < 0.001). Juvenile recruitment (<75.0 cm straight carapace length; SCL) from the north-western Caribbean increased from 12% to 38% while recruitment from the eastern Caribbean region decreased from 46% to 20% between 2006-2007 and 2015-2016. Furthermore, the product of the population growth rate and adult female abundance was a significant predictor for population composition in 2015-2016. Our results may reflect early warning signals of declining reproductive output at eastern Caribbean rookeries, potential displacement effects of smaller rookeries by larger rookeries, and advocate for genetic monitoring as a useful method for monitoring trends in juvenile megafauna. Furthermore, these findings underline the need for adequate conservation of juvenile developmental habitats and a deeper understanding of the interactions between megafaunal population dynamics in different habitats.
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Affiliation(s)
- Jurjan P van der Zee
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborg 7, 9747 AG, Groningen, The Netherlands. .,Wageningen Marine Research, Ankerpark 27, 1781 AG, Den Helder, The Netherlands.
| | - Marjolijn J A Christianen
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborg 7, 9747 AG, Groningen, The Netherlands.,Aquatic Ecology and Water Quality Management Group, Wageningen University & Research, P.O. Box 47, 6700 AA, Wageningen, The Netherlands
| | - Mabel Nava
- Sea Turtle Conservation Bonaire, P.O. Box 492, Kaya Korona 53, Kralendijk, Bonaire, The Netherlands
| | - Ximena Velez-Zuazo
- Sea Turtle Conservation Bonaire, P.O. Box 492, Kaya Korona 53, Kralendijk, Bonaire, The Netherlands.,Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Wensi Hao
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborg 7, 9747 AG, Groningen, The Netherlands
| | - Martine Bérubé
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborg 7, 9747 AG, Groningen, The Netherlands.,Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA, 02657, USA
| | | | - Michael Hiwat
- WWF Guianas, Henck Arronstraat 63, Paramaribo, Suriname
| | - Rachel Berzins
- ONCFS Guyane, Campus Agronomique, BP316, 97379, Kourou, French Guiana
| | - Johan Chevalier
- RNN Amana, Réserve Naturelle de l'Amana, Maison de la Réserve, 270 Avenue 31 Décembre, 97319, Awala-Yalimapo, French Guiana
| | - Damien Chevallier
- Université de Strasbourg, CNRS, IPHC, 23 Rue Becquerel, UMR, 7178, Strasbourg, France
| | - Marie-Clélia Lankester
- RNN Amana, Réserve Naturelle de l'Amana, Maison de la Réserve, 270 Avenue 31 Décembre, 97319, Awala-Yalimapo, French Guiana
| | - Karen A Bjorndal
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL, 32611, USA
| | - Alan B Bolten
- Archie Carr Center for Sea Turtle Research and Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL, 32611, USA
| | - Leontine E Becking
- Wageningen Marine Research, Ankerpark 27, 1781 AG, Den Helder, The Netherlands.,Marine Animal Ecology Group, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Per J Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborg 7, 9747 AG, Groningen, The Netherlands.,Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA, 02657, USA
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13
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Rivera-León VE, Urbán J, Mizroch S, Brownell RL, Oosting T, Hao W, Palsbøll PJ, Bérubé M. Long-term isolation at a low effective population size greatly reduced genetic diversity in Gulf of California fin whales. Sci Rep 2019; 9:12391. [PMID: 31455830 PMCID: PMC6712047 DOI: 10.1038/s41598-019-48700-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 08/06/2019] [Indexed: 11/09/2022] Open
Abstract
The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (Nem between 0.89-1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.
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Affiliation(s)
- Vania E Rivera-León
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Jorge Urbán
- Departamento de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Km 5.5 Carretera al Sur, 23081, La Paz, Baja California Sur, Mexico
| | - Sally Mizroch
- Blue Sea Research PO Box 15805, Seattle, WA, 98115, United States of America
| | - Robert L Brownell
- Southwest Fisheries Science Center, NOAA Fisheries, 34500 Highway 1, Monterey, CA, 93940, United States of America
| | - Tom Oosting
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Wensi Hao
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Per J Palsbøll
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. .,Centre for Coastal Studies, 5 Holway Avenue, Provincetown, Massachusetts, 02657, United States of America.
| | - Martine Bérubé
- Marine Evolution and Conservation, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. .,Centre for Coastal Studies, 5 Holway Avenue, Provincetown, Massachusetts, 02657, United States of America.
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14
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Tollis M, Robbins J, Webb AE, Kuderna LFK, Caulin AF, Garcia JD, Bèrubè M, Pourmand N, Marques-Bonet T, O’Connell MJ, Palsbøll PJ, Maley CC. Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). Mol Biol Evol 2019; 36:1746-1763. [PMID: 31070747 PMCID: PMC6657726 DOI: 10.1093/molbev/msz099] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cetaceans are a clade of highly specialized aquatic mammals that include the largest animals that have ever lived. The largest whales can have ∼1,000× more cells than a human, with long lifespans, leaving them theoretically susceptible to cancer. However, large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans-an observation known as Peto's Paradox. To investigate the genomic bases of gigantism and other cetacean adaptations, we generated a de novo genome assembly for the humpback whale (Megaptera novaeangliae) and incorporated the genomes of ten cetacean species in a comparative analysis. We found further evidence that rorquals (family Balaenopteridae) radiated during the Miocene or earlier, and inferred that perturbations in abundance and/or the interocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. Genomic analyses shed light on the molecular mechanisms underlying cetacean traits, including gigantism, and will contribute to the development of future targets for human cancer therapies.
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Affiliation(s)
- Marc Tollis
- Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | | | - Andrew E Webb
- Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA
| | | | - Aleah F Caulin
- Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, PA
| | | | - Martine Bèrubè
- Center for Coastal Studies, Provincetown, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Nader Pourmand
- Jack Baskin School of Engineering, University of California Santa Cruz, Santa Cruz, CA
| | - Tomas Marques-Bonet
- Instituto de Biologia Evolutiva (UPF-CSIC), PRBB, Barcelona, Spain
- CNAG‐CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Barcelona, Spain
| | - Mary J O’Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Per J Palsbøll
- Center for Coastal Studies, Provincetown, MA
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Carlo C Maley
- Biodesign Institute, Arizona State University, Tempe, AZ
- School of Life Sciences, Arizona State University, Tempe, AZ
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15
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Schleimer A, Ramp C, Delarue J, Carpentier A, Bérubé M, Palsbøll PJ, Sears R, Hammond PS. Decline in abundance and apparent survival rates of fin whales ( Balaenoptera physalus) in the northern Gulf of St. Lawrence. Ecol Evol 2019; 9:4231-4244. [PMID: 31016001 PMCID: PMC6468087 DOI: 10.1002/ece3.5055] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/16/2019] [Accepted: 02/25/2019] [Indexed: 11/06/2022] Open
Abstract
Estimates of abundance and survivorship provide quantifiable measures to monitor populations and to define and understand their conservation status. This study investigated changes in abundance and survival rates of fin whales (Balaenoptera physalus) in the northern Gulf of St. Lawrence in the context of anthropogenic pressures and changing environmental conditions. A long-term data set, consisting of 35 years of photo-identification surveys and comprising more than 5,000 identifications of 507 individuals, formed the basis of this mark-recapture study. Based on model selection using corrected Akaike Information Criterion, the most parsimonious Cormack-Jolly-Seber model included a linear temporal trend in noncalf apparent survival rates with a sharp decline in the last 5 years of the study and a median survival rate of 0.946 (95% confidence interval (CI) 0.910-0.967). To account for capture heterogeneity due to divergent patterns of site fidelity, agglomerative hierarchical cluster analysis was employed to categorize individuals based on their annual and survey site fidelity indices. However, the negative trend in survivorship remained and was corroborated by a significant decline in the estimated super-population size from 335 (95% CI 321-348) individuals in 2004-2010 to 291 (95% CI 270-312) individuals in 2010-2016. Concurrently, a negative trend was estimated in recruitment to the population, supported by a sharp decrease in the number of observed calves. Ship strikes and changes in prey availability are potential drivers of the observed decline in fin whale abundance. The combination of clustering methods with mark-recapture represents a flexible way to investigate the effects of site fidelity on demographic variables and is broadly applicable to other individual-based studies.
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Affiliation(s)
- Anna Schleimer
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsFifeUK
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Mingan Island Cetacean StudySt LambertQuébecCanada
| | - Christian Ramp
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsFifeUK
- Mingan Island Cetacean StudySt LambertQuébecCanada
| | | | | | - Martine Bérubé
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusetts
| | - Per J. Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Center for Coastal StudiesProvincetownMassachusetts
| | | | - Philip S. Hammond
- Sea Mammal Research Unit, Scottish Oceans InstituteUniversity of St AndrewsFifeUK
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16
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Fietz K, Rye Hintze CO, Skovrind M, Kjærgaard Nielsen T, Limborg MT, Krag MA, Palsbøll PJ, Hestbjerg Hansen L, Rask Møller P, Gilbert MTP. Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species. Microbiome 2018; 6:82. [PMID: 29720271 PMCID: PMC5932900 DOI: 10.1186/s40168-018-0467-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 03/26/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ecological adaptive potential are classically viewed at the genetic level, it has recently been argued that their microbiomes may also contribute to population genetic divergence. We explored whether this might be plausible along the well-described environmental gradient of the Baltic Sea in two species of sand lance (Ammodytes tobianus and Hyperoplus lanceolatus). Specifically, we assessed both their population genetic and gut microbial composition variation and investigated not only which environmental parameters correlate with the observed variation, but whether host genome also correlates with microbiome variation. RESULTS We found a clear genetic structure separating the high-salinity North Sea from the low-salinity Baltic Sea sand lances. The observed genetic divergence was not simply a function of isolation by distance, but correlated with environmental parameters, such as salinity, sea surface temperature, and, in the case of A. tobianus, possibly water microbiota. Furthermore, we detected two distinct genetic groups in Baltic A. tobianus that might represent sympatric spawning types. Investigation of possible drivers of gut microbiome composition variation revealed that host species identity was significantly correlated with the microbial community composition of the gut. A potential influence of host genetic factors on gut microbiome composition was further confirmed by the results of a constrained analysis of principal coordinates. The host genetic component was among the parameters that best explain observed variation in gut microbiome composition. CONCLUSIONS Our findings have relevance for the population structure of two commercial species but also provide insights into potentially relevant genomic and microbial factors with regards to sand lance adaptation across the North Sea-Baltic Sea environmental gradient. Furthermore, our findings support the hypothesis that host genetics may play a role in regulating the gut microbiome at both the interspecific and intraspecific levels. As sequencing costs continue to drop, we anticipate that future studies that include full genome and microbiome sequencing will be able to explore the full relationship and its potential adaptive implications for these species.
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Affiliation(s)
- Katharina Fietz
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
- Marine Evolution and Conservation, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
| | - Christian Olaf Rye Hintze
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Mikkel Skovrind
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Tue Kjærgaard Nielsen
- Department of Environmental Science, Environmental Microbial Genomics Group, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Morten T Limborg
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Marcus A Krag
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Per J Palsbøll
- Marine Evolution and Conservation, Faculty of Science and Engineering, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lars Hestbjerg Hansen
- Department of Environmental Science, Environmental Microbial Genomics Group, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Peter Rask Møller
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, Section for Evolutionary Genomics, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.
- NTNU University Museum, 7491, Trondheim, Norway.
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17
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Fountain ED, Kang JK, Tempel DJ, Palsbøll PJ, Pauli JN, Zachariah Peery M. Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agroecosystem. Mol Ecol 2017; 27:41-53. [DOI: 10.1111/mec.14388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/11/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Emily D. Fountain
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
| | - Jung koo Kang
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
- Marine Evolution and Conservation Groningen Institute of Evolutionary Life Sciences University of Groningen Groningen The Netherlands
- Center of Quantitative Sciences in Biomedicine Department of Mathematics North Carolina State University Raleigh NC USA
| | - Douglas J. Tempel
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
| | - Per J. Palsbøll
- Marine Evolution and Conservation Groningen Institute of Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI USA
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18
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Fietz K, Galatius A, Teilmann J, Dietz R, Frie AK, Klimova A, Palsbøll PJ, Jensen LF, Graves JA, Hoffman JI, Olsen MT. Shift of grey seal subspecies boundaries in response to climate, culling and conservation. Mol Ecol 2017; 25:4097-112. [PMID: 27616353 DOI: 10.1111/mec.13748] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/06/2016] [Accepted: 06/22/2016] [Indexed: 12/01/2022]
Abstract
Identifying the processes that drive changes in the abundance and distribution of natural populations is a central theme in ecology and evolution. Many species of marine mammals have experienced dramatic changes in abundance and distribution due to climatic fluctuations and anthropogenic impacts. However, thanks to conservation efforts, some of these species have shown remarkable population recovery and are now recolonizing their former ranges. Here, we use zooarchaeological, demographic and genetic data to examine processes of colonization, local extinction and recolonization of the two northern European grey seal subspecies inhabiting the Baltic Sea and North Sea. The zooarchaeological and genetic data suggest that the two subspecies diverged shortly after the formation of the Baltic Sea approximately 4200 years bp, probably through a gradual shift to different breeding habitats and phenologies. By comparing genetic data from 19th century pre-extinction material with that from seals currently recolonizing their past range, we observed a marked spatiotemporal shift in subspecies boundaries, with increasing encroachment of North Sea seals on areas previously occupied by the Baltic Sea subspecies. Further, both demographic and genetic data indicate that the two subspecies have begun to overlap geographically and are hybridizing in a narrow contact zone. Our findings provide new insights into the processes of colonization, extinction and recolonization and have important implications for the management of grey seals across northern Europe.
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Affiliation(s)
- Katharina Fietz
- Evolutionary Genomics Section, Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.,Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anders Galatius
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Jonas Teilmann
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | - Rune Dietz
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
| | | | - Anastasia Klimova
- Department of Animal Behaviour, University of Bielefeld, PO Box 10 01 31, 33501 Bielefeld, Germany
| | - Per J Palsbøll
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lasse F Jensen
- Fisheries and Maritime Museum, Tarphagevej 2, DK-6710 Esbjerg V, Denmark
| | - Jeff A Graves
- Scottish Oceans Institute, School of Biology, University of St Andrews, Fife KY16 9TH, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, PO Box 10 01 31, 33501 Bielefeld, Germany
| | - Morten Tange Olsen
- Evolutionary Genomics Section, Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
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19
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Cabrera AA, Palsbøll PJ. Inferring past demographic changes from contemporary genetic data: A simulation-based evaluation of the ABC methods implemented indiyabc. Mol Ecol Resour 2017; 17:e94-e110. [DOI: 10.1111/1755-0998.12696] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Andrea A. Cabrera
- Marine Evolution and Conservation; Groningen Institute of Evolutionary Life Sciences; University of Groningen; Groningen The Netherlands
| | - Per J. Palsbøll
- Marine Evolution and Conservation; Groningen Institute of Evolutionary Life Sciences; University of Groningen; Groningen The Netherlands
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20
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Reid BN, Thiel RP, Palsbøll PJ, Peery MZ. Linking Genetic Kinship and Demographic Analyses to Characterize Dispersal: Methods and Application to Blanding’s Turtle. J Hered 2016; 107:603-614. [DOI: 10.1093/jhered/esw052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/11/2016] [Indexed: 11/14/2022] Open
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21
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Fountain ED, Pauli JN, Reid BN, Palsbøll PJ, Peery MZ. Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates. Mol Ecol Resour 2016; 16:966-78. [DOI: 10.1111/1755-0998.12519] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 02/10/2016] [Accepted: 02/11/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Emily D. Fountain
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI 53706 USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI 53706 USA
| | - Brendan N. Reid
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI 53706 USA
| | - Per J. Palsbøll
- Marine Evolution and Conservation Groningen Institute of Evolutionary Life Sciences University of Groningen Groningen9747 AG The Netherlands
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison Madison WI 53706 USA
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22
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Best PB, Elwen SH, Palsbøll PJ, Thornton M, Austin E, Vinding K. Possible non-offspring nursing in the southern right whale,Eubalaena australis. J Mammal 2015. [DOI: 10.1093/jmammal/gyv042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Ramp C, Delarue J, Palsbøll PJ, Sears R, Hammond PS. Adapting to a warmer ocean--seasonal shift of baleen whale movements over three decades. PLoS One 2015; 10:e0121374. [PMID: 25785462 PMCID: PMC4364899 DOI: 10.1371/journal.pone.0121374] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 02/11/2015] [Indexed: 11/19/2022] Open
Abstract
Global warming poses particular challenges to migratory species, which face changes to the multiple environments occupied during migration. For many species, the timing of migration between summer and winter grounds and also within-season movements are crucial to maximise exploitation of temporarily abundant prey resources in feeding areas, themselves adapting to the warming planet. We investigated the temporal variation in the occurrence of fin (Balaenoptera physalus) and humpback whales (Megaptera novaeangliae) in a North Atlantic summer feeding ground, the Gulf of St. Lawrence (Canada), from 1984 to 2010 using a long-term study of individually identifiable animals. These two sympatric species both shifted their date of arrival at a previously undocumented rate of more than 1 day per year earlier over the study period thus maintaining the approximate 2-week difference in arrival of the two species and enabling the maintenance of temporal niche separation. However, the departure date of both species also shifted earlier but at different rates resulting in increasing temporal overlap over the study period indicating that this separation may be starting to erode. Our analysis revealed that the trend in arrival was strongly related to earlier ice break-up and rising sea surface temperature, likely triggering earlier primary production. The observed changes in phenology in response to ocean warming are a remarkable example of phenotypic plasticity and may partly explain how baleen whales were able to survive a number of changes in climate over the last several million years. However, it is questionable whether the observed rate of change in timing can be maintained. Substantial modification to the distribution or annual life cycle of these species might be required to keep up with the ongoing warming of the oceans.
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Affiliation(s)
- Christian Ramp
- Mingan Island Cetacean Study, St. Lambert, Quebec, Canada
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, St. Andrews, United Kingdom
- * E-mail:
| | - Julien Delarue
- Mingan Island Cetacean Study, St. Lambert, Quebec, Canada
| | - Per J. Palsbøll
- Marine Evolution and Conservation, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Richard Sears
- Mingan Island Cetacean Study, St. Lambert, Quebec, Canada
| | - Philip S. Hammond
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St. Andrews, St. Andrews, United Kingdom
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24
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Olsen MT, Robbins J, Bérubé M, Rew MB, Palsbøll PJ. Utility of telomere length measurements for age determination of humpback whales. NAMMCOSP 2014. [DOI: 10.7557/3.3194] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
This study examines the applicability of telomere length measurements by quantitative PCR as a tool for minimally invasive age determination of free-ranging cetaceans. We analysed telomere length in skin samples from 28 North Atlantic humpback whales (Megaptera novaeangliae), ranging from 0 to 26 years of age. The results suggested a significant correlation between telomere length and age in humpback whales. However, telomere length was highly variable among individuals of similar age, suggesting that telomere length measured by quantitative PCR is an imprecise determinant of age in humpback whales. The observed variation in individual telomere length was found to be a function of both experimental and biological variability, with the latter perhaps reflecting patterns of inheritance, resource allocation trade-offs, and stochasticity of the marine environment.
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25
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Olsen MT, Pampoulie C, Daníelsdóttir AK, Lidh E, Bérubé M, Víkingsson GA, Palsbøll PJ. Fin whale MDH-1 and MPI allozyme variation is not reflected in the corresponding DNA sequences. Ecol Evol 2014; 4:1787-803. [PMID: 24963377 PMCID: PMC4063476 DOI: 10.1002/ece3.1046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 11/07/2022] Open
Abstract
The appeal of genetic inference methods to assess population genetic structure and guide management efforts is grounded in the correlation between the genetic similarity and gene flow among populations. Effects of such gene flow are typically genomewide; however, some loci may appear as outliers, displaying above or below average genetic divergence relative to the genomewide level. Above average population, genetic divergence may be due to divergent selection as a result of local adaptation. Consequently, substantial efforts have been directed toward such outlying loci in order to identify traits subject to local adaptation. Here, we report the results of an investigation into the molecular basis of the substantial degree of genetic divergence previously reported at allozyme loci among North Atlantic fin whale (Balaenoptera physalus) populations. We sequenced the exons encoding for the two most divergent allozyme loci (MDH-1 and MPI) and failed to detect any nonsynonymous substitutions. Following extensive error checking and analysis of additional bioinformatic and morphological data, we hypothesize that the observed allozyme polymorphisms may reflect phenotypic plasticity at the cellular level, perhaps as a response to nutritional stress. While such plasticity is intriguing in itself, and of fundamental evolutionary interest, our key finding is that the observed allozyme variation does not appear to be a result of genetic drift, migration, or selection on the MDH-1 and MPI exons themselves, stressing the importance of interpreting allozyme data with caution. As for North Atlantic fin whale population structure, our findings support the low levels of differentiation found in previous analyses of DNA nucleotide loci.
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Affiliation(s)
- Morten Tange Olsen
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden
| | | | | | - Emmelie Lidh
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden
| | - Martine Bérubé
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden ; Marine Evolution and Conservation, Centre for Ecological and Evolutionary Studies, University of Groningen PO Box 11103, 9700 CC, Groningen, The Netherlands
| | | | - Per J Palsbøll
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University Svante Arrhenius Väg 20C, S-106 91 Stockholm, Sweden ; Marine Evolution and Conservation, Centre for Ecological and Evolutionary Studies, University of Groningen PO Box 11103, 9700 CC, Groningen, The Netherlands
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Ryan C, McHugh B, Boyle B, McGovern E, Bérubé M, Lopez-Suárez P, Elfes CT, Boyd DT, Ylitalo GM, Van Blaricom GR, Clapham PJ, Robbins J, Palsbøll PJ, O’Connor I, Berrow SD. Levels of persistent organic pollutants in eastern North Atlantic humpback whales. ENDANGER SPECIES RES 2013. [DOI: 10.3354/esr00545] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Peery MZ, Reid BN, Kirby R, Stoelting R, Doucet-Bëer E, Robinson S, Vásquez-Carrillo C, Pauli JN, Palsbøll PJ. More precisely biased: increasing the number of markers is not a silver bullet in genetic bottleneck testing. Mol Ecol 2013; 22:3451-7. [DOI: 10.1111/mec.12394] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- M. Zachariah Peery
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706 USA
| | - Brendan N. Reid
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706 USA
| | - Rebecca Kirby
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706 USA
| | - Ricka Stoelting
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706 USA
| | - Elena Doucet-Bëer
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706 USA
| | - Stacie Robinson
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706 USA
| | - Catalina Vásquez-Carrillo
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706 USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706 USA
| | - Per J. Palsbøll
- Marine Evolution and Conservation; Centre of Evolutionary and Ecological Studies; University of Groningen; PO Box 11103 CC Groningen The Netherlands
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Abstract
Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.
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Affiliation(s)
- Per J Palsbøll
- Marine Evolution and Conservation, Centre of Evolutionary and Ecological Studies, University of Groningen, PO Box 11103 CC, Groningen, The Netherlands.
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29
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Olsen MT, Bérubé M, Robbins J, Palsbøll PJ. Empirical evaluation of humpback whale telomere length estimates; quality control and factors causing variability in the singleplex and multiplex qPCR methods. BMC Genet 2012; 13:77. [PMID: 22954451 PMCID: PMC3489520 DOI: 10.1186/1471-2156-13-77] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Accepted: 08/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Telomeres, the protective cap of chromosomes, have emerged as powerful markers of biological age and life history in model and non-model species. The qPCR method for telomere length estimation is one of the most common methods for telomere length estimation, but has received recent critique for being too error-prone and yielding unreliable results. This critique coincides with an increasing awareness of the potentials and limitations of the qPCR technique in general and the proposal of a general set of guidelines (MIQE) for standardization of experimental, analytical, and reporting steps of qPCR. In order to evaluate the utility of the qPCR method for telomere length estimation in non-model species, we carried out four different qPCR assays directed at humpback whale telomeres, and subsequently performed a rigorous quality control to evaluate the performance of each assay. RESULTS Performance differed substantially among assays and only one assay was found useful for telomere length estimation in humpback whales. The most notable factors causing these inter-assay differences were primer design and choice of using singleplex or multiplex assays. Inferred amplification efficiencies differed by up to 40% depending on assay and quantification method, however this variation only affected telomere length estimates in the worst performing assays. CONCLUSION Our results suggest that seemingly well performing qPCR assays may contain biases that will only be detected by extensive quality control. Moreover, we show that the qPCR method for telomere length estimation can be highly precise and accurate, and thus suitable for telomere measurement in non-model species, if effort is devoted to optimization at all experimental and analytical steps. We conclude by highlighting a set of quality controls which may serve for further standardization of the qPCR method for telomere length estimation, and discuss some of the factors that may cause variation in qPCR experiments.
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Affiliation(s)
- Morten Tange Olsen
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University, Stockholm, S-106 91, Sweden.
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Peery MZ, Kirby R, Reid BN, Stoelting R, Doucet-Bëer E, Robinson S, Vásquez-Carrillo C, Pauli JN, Palsbøll PJ. Reliability of genetic bottleneck tests for detecting recent population declines. Mol Ecol 2012; 21:3403-18. [PMID: 22646281 DOI: 10.1111/j.1365-294x.2012.05635.x] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.
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Affiliation(s)
- M Zachariah Peery
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706, USA.
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Wiig Ø, Heide-Jørgensen MP, Lindqvist C, Laidre KL, Postma LD, Dueck L, Palsbøll PJ, Bachmann L. Recaptures of genotyped bowhead whales Balaena mysticetus in eastern Canada and West Greenland. ENDANGER SPECIES RES 2011. [DOI: 10.3354/esr00365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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32
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Rew MB, Robbins J, Mattila D, Palsbøll PJ, Bérube M. How many genetic markers to tag an individual? An empirical assessment of false matching rates among close relatives. Ecol Appl 2011; 21:877-887. [PMID: 21639051 DOI: 10.1890/10-0348.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Genetic identification of individuals is now commonplace, enabling the application of tagging methods to elusive species or species that cannot be tagged by traditional methods. A key aspect is determining the number of loci required to ensure that different individuals have non-matching multi-locus genotypes. Closely related individuals are of particular concern because of elevated matching probabilities caused by their recent co-ancestry. This issue may be addressed by increasing the number of loci to a level where full siblings (the relatedness category with the highest matching probability) are expected to have non-matching multi-locus genotypes. However, increasing the number of loci to meet this "full-sib criterion" greatly increases the laboratory effort, which in turn may increase the genotyping error rate resulting in an upward-biased mark-recapture estimate of abundance as recaptures are missed due to genotyping errors. We assessed the contribution of false matches from close relatives among 425 maternally related humpback whales, each genotyped at 20 microsatellite loci. We observed a very low (0.5-4%) contribution to falsely matching samples from pairs of first-order relatives (i.e., parent and offspring or full siblings). The main contribution to falsely matching individuals from close relatives originated from second-order relatives (e.g., half siblings), which was estimated at 9%. In our study, the total number of observed matches agreed well with expectations based upon the matching probability estimated for unrelated individuals, suggesting that the full-sib criterion is overly conservative, and would have required a 280% relative increase in effort. We suggest that, under most circumstances, the overall contribution to falsely matching samples from close relatives is likely to be low, and hence applying the full-sib criterion is unnecessary. In those cases where close relatives may present a significant issue, such as unrepresentative sampling, we propose three different genotyping strategies requiring only a modest increase in effort, which will greatly reduce the number of false matches due to the presence of related individuals.
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Affiliation(s)
- Mary Beth Rew
- Department of Environmental Science, Policy and Management, University of California, 137 Mulford Hall, Berkeley, California 94720-3110, USA
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33
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Olsen MT, Volny VH, Bérubé M, Dietz R, Lydersen C, Kovacs KM, Dodd RS, Palsbøll PJ. A simple route to single-nucleotide polymorphisms in a nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida hispida). Mol Ecol Resour 2011; 11 Suppl 1:9-19. [PMID: 21429159 DOI: 10.1111/j.1755-0998.2010.02941.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Morten Tange Olsen
- Evolutionary Genetics Group, Department of Genetics, Microbiology, and Toxicology, Stockholm University, Sweden.
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34
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Palsbøll PJ, Zachariah Peery M, Bérubé M. Detecting populations in the 'ambiguous' zone: kinship-based estimation of population structure at low genetic divergence. Mol Ecol Resour 2010; 10:797-805. [PMID: 21565091 DOI: 10.1111/j.1755-0998.2010.02887.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Identifying population structure is one of the most common and important objectives of spatial analyses using population genetic data. Population structure is detected either by rejecting the null hypothesis of a homogenous distribution of genetic variation, or by estimating low migration rates. Issues arise with most current population genetic inference methods when the genetic divergence is low among putative populations. Low levels of genetic divergence may be as a result of either high ongoing migration or historic high migration but no current, ongoing migration. We direct attention to recent developments in the use of the tempo-spatial distribution of closely related individuals to detect population structure or estimate current migration rates. These 'kinship-based' approaches complement more traditional population-based genetic inference methods by providing a means to detect population structure and estimate current migration rates when genetic divergence is low. However, for kinship-based methods to become widely adopted, formal estimation procedures applicable to a range of species life histories are needed.
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Affiliation(s)
- Per J Palsbøll
- Department of Genetics, Microbiology and Toxicology, Stockholm University, SE-106 91 Stockholm, Sweden Department of Forest and Wildlife Ecology, University of Wisconsin Madison, 1630 Linden Drive, Madison, WI 53706, USA
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35
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Peery MZ, Hall LA, Sellas A, Beissinger SR, Moritz C, Bérubé M, Raphael MG, Nelson SK, Golightly RT, McFarlane-Tranquilla L, Newman S, Palsbøll PJ. Genetic analyses of historic and modern marbled murrelets suggest decoupling of migration and gene flow after habitat fragmentation. Proc Biol Sci 2010; 277:697-706. [PMID: 19906669 PMCID: PMC2842750 DOI: 10.1098/rspb.2009.1666] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 10/19/2009] [Indexed: 11/12/2022] Open
Abstract
The dispersal of individuals among fragmented populations is generally thought to prevent genetic and demographic isolation, and ultimately reduce extinction risk. In this study, we show that a century of reduction in coastal old-growth forests, as well as a number of other environmental factors, has probably resulted in the genetic divergence of marbled murrelets (Brachyramphus marmoratus) in central California, despite the fact that 7 per cent of modern-sampled murrelets in this population were classified as migrants using genetic assignment tests. Genetic differentiation appears to persist because individuals dispersing from northern populations contributed relatively few young to the central California population, as indicated by the fact that migrants were much less likely to be members of parent-offspring pairs than residents (10.5% versus 45.4%). Moreover, a recent 1.4 per cent annual increase in the proportion of migrants in central California, without appreciable reproduction, may have masked an underlying decline in the resident population without resulting in demographic rescue. Our results emphasize the need to understand the behaviour of migrants and the extent to which they contribute offspring in order to determine whether dispersal results in gene flow and prevents declines in resident populations.
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Affiliation(s)
- M Zachariah Peery
- Department of Forest and Wildlife Ecology, 1630 Linden Drive Madison, University of Wisconsin-Madison, Madison, WI 53706, USA.
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36
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Hall LA, Palsbøll PJ, Beissinger SR, Harvey JT, Bérubé M, Raphael MG, Nelson SK, Golightly RT, McFarlane-Tranquilla L, Newman SH, Peery MZ. Characterizing dispersal patterns in a threatened seabird with limited genetic structure. Mol Ecol 2009; 18:5074-85. [PMID: 19912540 DOI: 10.1111/j.1365-294x.2009.04416.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic assignment methods provide an appealing approach for characterizing dispersal patterns on ecological time scales, but require sufficient genetic differentiation to accurately identify migrants and a large enough sample size of migrants to, for example, compare dispersal between sexes or age classes. We demonstrate that assignment methods can be rigorously used to characterize dispersal patterns in a marbled murrelet (Brachyramphus marmoratus) population from central California that numbers approximately 600 individuals and is only moderately differentiated (F(ST) approximately 0.03) from larger populations to the north. We used coalescent simulations to select a significance level that resulted in a low and approximately equal expected number of type I and II errors and then used this significance level to identify a population of origin for 589 individuals genotyped at 13 microsatellite loci. The proportion of migrants in central California was greatest during winter when 83% of individuals were classified as migrants compared to lower proportions during the breeding (6%) and post-breeding (8%) seasons. Dispersal was also biased toward young and female individuals, as is typical in birds. Migrants were rarely members of parent-offspring pairs, suggesting that they contributed few young to the central California population. A greater number of migrants than expected under equilibrium conditions, a lack of individuals with mixed ancestry, and a small number of potential source populations (two), likely allowed us to use assignment methods to rigorously characterize dispersal patterns for a population that was larger and less differentiated than typically thought required for the identification of migrants.
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37
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Abstract
Source-sink dynamics have been suggested to characterize the population structure of many species, but the prevalence of source-sink systems in nature is uncertain because of inherent challenges in estimating migration rates among populations. Migration rates are often difficult to estimate directly with demographic methods, and indirect genetic methods are subject to a variety of assumptions that are difficult to meet or to apply to evolutionary timescales. Furthermore, such methods cannot be rigorously applied to high-gene-flow species. Here, we employ genetic parentage assignments in conjunction with demographic simulations to infer the level of immigration into a putative sink population. We use individual-based demographic models to estimate expected distributions of parent-offspring dyads under competing sink and closed-population models. By comparing the actual number of parent-offspring dyads (identified from multilocus genetic profiles) in a random sample of individuals taken from a population to expectations under these two contrasting demographic models, it is possible to estimate the rate of immigration and test hypotheses related to the role of immigration on population processes on an ecological timescale. The difference in the expected number of parent-offspring dyads between the two population models was greatest when immigration into the sink population was high, indicating that unlike traditional population genetic inference models, the highest degree of statistical power is achieved for the approach presented here when migration rates are high. We used the proposed genetic parentage approach to demonstrate that a threatened population of Marbled Murrelets (Braclhyrarmphus marmotus) appears to be supplemented by a low level of immigration (approximately 2-6% annually) from other populations.
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Affiliation(s)
- M Zachariah Peery
- Department of Environmental Science, Policy and Management, 137 Mulfiord Hall, University of California, Berkeley, California 94720-3114, USA.
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Palsbøll PJ, Bérubé M, Larsen F. Could genetic diversity in eastern North Pacific gray whales reflect global historic abundance? Proc Natl Acad Sci U S A 2007; 104:E2; author reply E3. [PMID: 18093947 PMCID: PMC2409264 DOI: 10.1073/pnas.0710072105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Per J. Palsbøll
- *Department of Genetics, Microbiology, and Toxicology, Stockholm University, SE-106 91 Stockholm, Sweden; and
| | - Martine Bérubé
- *Department of Genetics, Microbiology, and Toxicology, Stockholm University, SE-106 91 Stockholm, Sweden; and
| | - Finn Larsen
- Department of Marine Fisheries, Danish Institute for Fisheries Research, Technical University of Denmark, Charlottenlund Castle, DK-2920 Charlottenlund, Denmark
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Pastene LA, Goto M, Kanda N, Zerbini AN, Kerem D, Watanabe K, Bessho Y, Hasegawa M, Nielsen R, Larsen F, Palsbøll PJ. Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Mol Ecol 2007; 16:1481-95. [PMID: 17391271 DOI: 10.1111/j.1365-294x.2007.03244.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
How do populations of highly mobile species inhabiting open environments become reproductively isolated and evolve into new species? We test the hypothesis that elevated ocean-surface temperatures can facilitate allopatry among pelagic populations and thus promote speciation. Oceanographic modelling has shown that increasing surface temperatures cause localization and reduction of upwelling, leading to fragmentation of feeding areas critical to pelagic species. We test our hypothesis by genetic analyses of populations of two closely related baleen whales, the Antarctic minke whale (Balaenoptera bonaerensis) and common minke whale (Balaenoptera acutorostrata) whose current distributions and migration patterns extent are largely determined by areas of consistent upwelling with high primary production. Phylogeographic and population genetic analyses of mitochondrial DNA control-region nucleotide sequences collected from 467 whales sampled in four different ocean basins were employed to infer the evolutionary relationship among populations of B. acutorostrata by rooting an intraspecific phylogeny with a population of B. bonaerensis. Our findings suggest that the two species diverged in the Southern Hemisphere less than 5 million years ago (Ma). This estimate places the speciation event during a period of extended global warming in the Pliocene. We propose that elevated ocean temperatures in the period facilitated allopatric speciation by disrupting the continuous belt of upwelling maintained by the Antarctic Circumpolar Current. Our analyses revealed that the current populations of B. acutorostrata likely diverged after the Pliocene some 1.5 Ma when global temperatures had decreased and presumably coinciding with the re-establishment of the polar-equatorial temperature gradient that ultimately drives upwelling. In most population samples, we detected genetic signatures of exponential population expansions, consistent with the notion of increasing carrying capacity after the Pliocene. Our hypothesis that prolonged periods of global warming facilitate speciation in pelagic marine species that depend on upwelling should be tested by comparative analyses in other pelagic species.
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Affiliation(s)
- Luis A Pastene
- Institute of Cetacean Research, 4-5 Toyomi-cho, Chuo-ku, Tokyo 104-0055, Japan.
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40
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Abstract
Global warming is predicted to affect the evolutionary potential of natural populations. We assessed genetic diversity of 25 populations of desert bighorn sheep (Ovis canadensis nelsoni) in southeastern California, where temperatures have increased and precipitation has decreased during the 20th century. Populations in low-elevation habitats had lower genetic diversity, presumably reflecting more fluctuations in population sizes and founder effects. Higher-elevation habitats acted as reservoirs of genetic diversity. However, genetic diversity was also affected by population connectivity, which has been disrupted by human development. Restoring population connectivity may be necessary to buffer the effects of climate change on this desert-adapted ungulate.
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Affiliation(s)
- Clinton W Epps
- Department of Environmental Science, Policy and Management, University of California Berkeley, 137 Mulford Hall #3114, Berkeley, CA 94720-3114, USA.
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Palsbøll PJ, Bérubé M, Allendorf FW. Identification of management units using population genetic data. Trends Ecol Evol 2007; 22:11-6. [PMID: 16982114 DOI: 10.1016/j.tree.2006.09.003] [Citation(s) in RCA: 439] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 07/27/2006] [Accepted: 09/07/2006] [Indexed: 10/24/2022]
Abstract
The identification of management units (MUs) is central to the management of natural populations and is crucial for monitoring the effects of human activity upon species abundance. Here, we propose that the identification of MUs from population genetic data should be based upon the amount of genetic divergence at which populations become demographically independent instead of the current criterion that focuses on rejecting panmixia. MU status should only be assigned when the observed estimate of genetic divergence is significantly greater than a predefined threshold value. We emphasize the need for a demographic interpretation of estimates of genetic divergence given that it is often the dispersal rate of individuals that is the parameter of immediate interest to conservationists rather than the historical amount of gene flow.
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Affiliation(s)
- Per J Palsbøll
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, California, 94720, USA.
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42
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Durnin ME, Palsbøll PJ, Ryder OA, McCullough DR. A reliable genetic technique for sex determination of giant panda (Ailuropoda melanoleuca) from non-invasively collected hair samples. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9196-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Palsbøll PJ, Bérubé M, Skaug HJ, Raymakers C. DNA registers of legally obtained wildlife and derived products as means to identify illegal takes. Conserv Biol 2006; 20:1284-93. [PMID: 16922244 DOI: 10.1111/j.1523-1739.2006.00429.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The exploitation and sale of wildlife species that are endangered in only part of their range present regulators with the critical challenge of separating legal from illegal takes. Wildlife DNA registers created from tissue samples of legally obtained individual wildlife specimens can address this problem by allowing managers to identify unregistered (presumably illegally obtained) specimens. We tested the effectiveness of the only current, fully operational wildlife DNA register of individual genetic profiles collected from legally caught minke whales (Balaenoptera acutorostrata). Twenty minke whale tissue samples collected at markets in Norway and 2 additional samples collected from beached minke whales in Denmark were genotyped at 12 loci used by the Norwegian minke whale DNA register Genetic profiles of these samples then were compared against the 2676 individual profiles deposited in the Norwegian register The high number of genetic markers used to identify individuals in our study allowed consistent matching of sample and reference profiles despite an overall error rate (due to experimental and interlaboratory data standardization) estimated at 0.015 per locus. Of the 22 test samples only the 2 Danish samples failed to match an existing profile in the Norwegian minke whale DNA register Our results show that the basic principle of wildlife DNA registers can work in a real-life situation. The strength of wildlife DNA registers lies in their ability to unambiguously identify unregistered specimens with the aid of sensitive genetic methods that enable analysis of highly processed or degraded tissue samples. Our study also highlights a number of methodological problems such as laboratory errors and interlaboratory data standardization, which need be addressed to ensure a successful implementation of wildlife DNA registers.
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Affiliation(s)
- Per J Palsbøll
- Environmental Science, Policy and Management, University of California Berkeley, 137 Mulford Hall, Berkeley, California 94720, USA.
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Bérubé M, Rew MB, Skaug H, Jørgensen H, Robbins J, Best P, Sears R, Palsbøll PJ. Polymorphic microsatellite loci isolated from humpback whale, Megaptera novaeangliae and fin whale, balaenoptera physalus. CONSERV GENET 2005. [DOI: 10.1007/s10592-005-9017-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Epps CW, Palsbøll PJ, Wehausen JD, Roderick GK, Ramey RR, McCullough DR. Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep. Ecol Lett 2005. [DOI: 10.1111/j.1461-0248.2005.00804.x] [Citation(s) in RCA: 339] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Palsbøll PJ, Bérubé M, Aguilar A, Notarbartolo-Di-Sciara G, Nielsen R. Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations. Evolution 2004; 58:670-5. [PMID: 15119452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Genetic divergence among conspecific subpopulations can be due to either low recurrent gene flow or recent divergence and no gene flow. Here we present a modification of an earlier method developed by Nielsen and Wakeley (2001), which accommodates a finite-site mutation model, to assess which of the two models of divergence is most likely given the observed data. We apply the method to nucleotide sequence data collected from the variable part of the mitochondrial control region in fin whales (Balaenoptera physalus) from the Atlantic coast off Spain and the Mediterranean Sea. Our estimations strongly favor a model of recurrent gene flow over a model of recent divergence and zero gene flow. We estimated the migration rate at two females per generation. While the estimated rate is high by evolutionary standards, exchange rates of this order of magnitude is low from an ecological and conservation perspective and entirely consistent with the current paucity of fin whale sightings in the Strait of Gibraltar today. Intensive commercial shore-based whaling during the 1920s removed substantial numbers of fin whales in the Strait of Gibraltar and this local population has seemingly since failed to recover.
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Affiliation(s)
- Per J Palsbøll
- Ecosystem Science Division--ESPM, University of California at Berkeley, 151 Hilgard Hall, 3110, Berkeley, California 94720-3110, USA.
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Palsbøll PJ, Bérubé M, Aguilar A, Notarbartolo-Di-Sciara G, Nielsen R. DISCERNING BETWEEN RECURRENT GENE FLOW AND RECENT DIVERGENCE UNDER A FINITE-SITE MUTATION MODEL APPLIED TO NORTH ATLANTIC AND MEDITERRANEAN SEA FIN WHALE (BALAENOPTERA PHYSALUS) POPULATIONS. Evolution 2004. [DOI: 10.1111/j.0014-3820.2004.tb01691.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Palsbøll PJ, Bérubé M, Aguilar A, Notarbartolo-Di-Sciara G, Nielsen R. DISCERNING BETWEEN RECURRENT GENE FLOW AND RECENT DIVERGENCE UNDER A FINITE-SITE MUTATION MODEL APPLIED TO NORTH ATLANTIC AND MEDITERRANEAN SEA FIN WHALE (BALAENOPTERA PHYSALUS) POPULATIONS. Evolution 2004. [DOI: 10.1554/02-529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Suarez AV, Bernard M, Tsutsui ND, Blackledge TA, Copren K, Sarnat EM, Wild AL, Getz WM, Starks PT, Will K, Palsbøll PJ, Hauber ME, Moritz C, Richman AD. Conflicts around a study of Mexican crops. Nature 2002; 417:897; author reply 897-8. [PMID: 12087376 DOI: 10.1038/417897a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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