1
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Doan K, Schnitzler A, Preston F, Griggo C, Lang G, Belhaoues F, Blaise E, Crégut-Bonnoure E, Frère S, Foucras S, Gardeisen A, Laurent A, Müller W, Picavet R, Puissant S, Yvinec JH, Pilot M. Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene. Mol Ecol 2023; 32:4627-4647. [PMID: 37337956 DOI: 10.1111/mec.17054] [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: 08/19/2022] [Revised: 05/20/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.
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Affiliation(s)
- Karolina Doan
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Annik Schnitzler
- UMR 7194 HNHP CNRS/MNHN/UPVD, Equipe NOMADE, Muséum national d'histoire naturelle, Paris, France
| | | | - Christophe Griggo
- Université Grenoble Alpes, Laboratoire EDYTEM, URM 5204 Bâtiment "Pôle Montagne", 5 bd de la mer Caspienne, France
| | - Gérard Lang
- Espace Chasse et Nature Chemin de Strasbourg, France
| | - Fabien Belhaoues
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Emilie Blaise
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Evelyne Crégut-Bonnoure
- Muséum Requien, Avignon; Laboratoire TRACES-UMR 5608, Université Toulouse-Jean Jaurès, Toulouse, France
| | - Stéphane Frère
- Inrap, UMR 7209 AASPE, Muséum National d'Histoire Naturelle, La Courneuve, France
| | | | - Armelle Gardeisen
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | | | - Werner Müller
- Laboratoire d'archéozoologie, Université de Neuchâtel, Avenue de Bellevaux 51, Neuchâtel, Switzerland
| | | | - Stéphane Puissant
- Muséum d'Histoire naturelle - Jardin de l'Arquebuse CS 73310 F-21033 Dijon Cedex, France
| | - Jean-Hervé Yvinec
- INRAP, UMR 7209 AASPE, Laboratoire d'archéozoologie de Compiègne, CRAVO, Compiègne, France
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
- School of Life Sciences, University of Lincoln, Lincoln, UK
- Faculty of Biology, University of Gdańsk, Gdańsk, Poland
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2
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Spatola GJ, Buckley RM, Dillon M, Dutrow EV, Betz JA, Pilot M, Parker HG, Bogdanowicz W, Thomas R, Chyzhevskyi I, Milinevsky G, Kleiman N, Breen M, Ostrander EA, Mousseau TA. The dogs of Chernobyl: Demographic insights into populations inhabiting the nuclear exclusion zone. Sci Adv 2023; 9:eade2537. [PMID: 36867701 PMCID: PMC9984172 DOI: 10.1126/sciadv.ade2537] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The 1986 Chernobyl nuclear disaster initiated a series of catastrophic events resulting in long-term and widespread environmental contamination. We characterize the genetic structure of 302 dogs representing three free-roaming dog populations living within the power plant itself, as well as those 15 to 45 kilometers from the disaster site. Genome-wide profiles from Chernobyl, purebred and free-breeding dogs, worldwide reveal that the individuals from the power plant and Chernobyl City are genetically distinct, with the former displaying increased intrapopulation genetic similarity and differentiation. Analysis of shared ancestral genome segments highlights differences in the extent and timing of western breed introgression. Kinship analysis reveals 15 families, with the largest spanning all collection sites within the radioactive exclusion zone, reflecting migration of dogs between the power plant and Chernobyl City. This study presents the first characterization of a domestic species in Chernobyl, establishing their importance for genetic studies into the effects of exposure to long-term, low-dose ionizing radiation.
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Affiliation(s)
- Gabriella J Spatola
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megan Dillon
- North Carolina State University, Raleigh NC 27695, USA
| | - Emily V Dutrow
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Heidi G Parker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Rachel Thomas
- North Carolina State University, Raleigh NC 27695, USA
| | | | - Gennadi Milinevsky
- Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- International Center of Future Science, College of Physics, Jilin University, Changchun 130012, China
| | | | - Matthew Breen
- North Carolina State University, Raleigh NC 27695, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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3
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [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: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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4
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Heino MT, Nyman T, Palo JU, Harmoinen J, Valtonen M, Pilot M, Översti S, Salmela E, Kunnasranta M, Väinölä R, Hoelzel AR, Aspi J. Museum specimens of a landlocked pinniped reveal recent loss of genetic diversity and unexpected population connections. Ecol Evol 2023; 13:e9720. [PMID: 36699566 PMCID: PMC9849707 DOI: 10.1002/ece3.9720] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023] Open
Abstract
The Saimaa ringed seal (Pusa hispida saimensis) is endemic to Lake Saimaa in Finland. The subspecies is thought to have originated when parts of the ringed seal population of the Baltic region were trapped in lakes emerging due to postglacial bedrock rebound around 9000 years ago. During the 20th century, the population experienced a drastic human-induced bottleneck. Today encompassing a little over 400 seals with extremely low genetic diversity, it is classified as endangered. We sequenced sections of the mitochondrial control region from 60 up to 125-years-old museum specimens of the Saimaa ringed seal. The generated dataset was combined with publicly available sequences. We studied how genetic variation has changed through time in this subspecies and how it is phylogenetically related to other ringed seal populations from the Baltic Sea, Lake Ladoga, North America, Svalbard, and the White Sea. We observed temporal fluctuations in haplotype frequencies and loss of haplotypes accompanied by a recent reduction in female effective population size. In apparent contrast with the traditionally held view of the Baltic origin of the population, the Saimaa ringed seal mtDNA variation also shows affinities to North American ringed seals. Our results suggest that the Saimaa ringed seal has experienced recent genetic drift associated with small population size. The results further suggest that extant Baltic ringed seal is not representative of the ancestral population of the Saimaa ringed seal, which calls for re-evaluation of the deep history of this subspecies.
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Affiliation(s)
- Matti T. Heino
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland,Department of Forensic MedicineUniversity of HelsinkiHelsinkiFinland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Jukka U. Palo
- Department of Forensic MedicineUniversity of HelsinkiHelsinkiFinland,Forensic Chemistry Unit/Forensic GeneticsFinnish Institute for Health and WelfareHelsinkiFinland
| | - Jenni Harmoinen
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland,Wildlife Ecology GroupNatural Resources Institute FinlandHelsinkiFinland
| | - Mia Valtonen
- Wildlife Ecology GroupNatural Resources Institute FinlandHelsinkiFinland,Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland,Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Małgorzata Pilot
- School of Biological and Biomedical SciencesDurham UniversityDurhamUK,Museum and Institute of ZoologyPolish Academy of SciencesGdańskPoland,Faculty of BiologyUniversity of GdańskGdańskPoland
| | - Sanni Översti
- Transmission, Infection, Diversification and Evolution GroupMax‐Planck Institute for the Science of Human HistoryJenaGermany,Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | - Elina Salmela
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland,Department of Biology, Faculty of ScienceUniversity of TurkuTurkuFinland
| | - Mervi Kunnasranta
- University of Eastern FinlandJoensuuFinland,Natural Resources Institute FinlandJoensuuFinland
| | - Risto Väinölä
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | | | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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5
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Hammond A, Rowland T, Mills DS, Pilot M. Comparison of behavioural tendencies between “dangerous dogs” and other domestic dog breeds – Evolutionary context and practical implications. Evol Appl 2022; 15:1806-1819. [DOI: 10.1111/eva.13479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 12/20/2022] Open
Affiliation(s)
- Alexa Hammond
- School of Life Sciences University of Lincoln Lincoln UK
| | - Thomas Rowland
- School of Life Sciences University of Lincoln Lincoln UK
| | | | - Małgorzata Pilot
- School of Life Sciences University of Lincoln Lincoln UK
- Museum and Institute of Zoology Polish Academy of Sciences Gdańsk Poland
- Faculty of Biology University of Gdańsk Gdańsk Poland
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6
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Bergström A, Stanton DWG, Taron UH, Frantz L, Sinding MHS, Ersmark E, Pfrengle S, Cassatt-Johnstone M, Lebrasseur O, Girdland-Flink L, Fernandes DM, Ollivier M, Speidel L, Gopalakrishnan S, Westbury MV, Ramos-Madrigal J, Feuerborn TR, Reiter E, Gretzinger J, Münzel SC, Swali P, Conard NJ, Carøe C, Haile J, Linderholm A, Androsov S, Barnes I, Baumann C, Benecke N, Bocherens H, Brace S, Carden RF, Drucker DG, Fedorov S, Gasparik M, Germonpré M, Grigoriev S, Groves P, Hertwig ST, Ivanova VV, Janssens L, Jennings RP, Kasparov AK, Kirillova IV, Kurmaniyazov I, Kuzmin YV, Kosintsev PA, Lázničková-Galetová M, Leduc C, Nikolskiy P, Nussbaumer M, O'Drisceoil C, Orlando L, Outram A, Pavlova EY, Perri AR, Pilot M, Pitulko VV, Plotnikov VV, Protopopov AV, Rehazek A, Sablin M, Seguin-Orlando A, Storå J, Verjux C, Zaibert VF, Zazula G, Crombé P, Hansen AJ, Willerslev E, Leonard JA, Götherström A, Pinhasi R, Schuenemann VJ, Hofreiter M, Gilbert MTP, Shapiro B, Larson G, Krause J, Dalén L, Skoglund P. Grey wolf genomic history reveals a dual ancestry of dogs. Nature 2022; 607:313-320. [PMID: 35768506 PMCID: PMC9279150 DOI: 10.1038/s41586-022-04824-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 08/27/2021] [Accepted: 04/28/2022] [Indexed: 01/01/2023]
Abstract
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.
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Affiliation(s)
- Anders Bergström
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
| | - David W G Stanton
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Laurent Frantz
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Molly Cassatt-Johnstone
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ophélie Lebrasseur
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Morgane Ollivier
- University of Rennes, CNRS, ECOBIO (Ecosystèmes, biodiversité, évolution)-UMR 6553, Rennes, France
| | - Leo Speidel
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.,Genetics Institute, University College London, London, UK
| | | | - Michael V Westbury
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Tatiana R Feuerborn
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,The Qimmeq Project, University of Greenland, Nuuk, Greenland.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Joscha Gretzinger
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Susanne C Münzel
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Pooja Swali
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas J Conard
- Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Christian Carøe
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Anna Linderholm
- Centre for Palaeogenetics, Stockholm, Sweden.,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Texas A&M University, College Station, TX, USA.,Department of Geological Sciences, Stockholm University, Stockholm, Sweden
| | | | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris Baumann
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Geosciences and Geography, Faculty of Science, University of Helsinki, Helsinki, Finland
| | | | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Ruth F Carden
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Sergey Fedorov
- North-Eastern Federal University, Yakutsk, Russian Federation
| | | | | | | | - Pam Groves
- University of Alaska, Fairbanks, AK, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum Bern, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | | | | | - Richard P Jennings
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Aleksei K Kasparov
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | - Irina V Kirillova
- Ice Age Museum, Shidlovskiy National Alliance 'Ice Age', Moscow, Russian Federation
| | - Islam Kurmaniyazov
- Department of Archaeology, Ethnology and Museology, Al-Farabi Kazakh State University, Almaty, Kazakhstan
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | - Pavel Nikolskiy
- Geological Institute, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Cóilín O'Drisceoil
- National Monuments Service, Department of Housing, Local Government and Heritage, Dublin, Ireland
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Elena Y Pavlova
- Arctic & Antarctic Research Institute, St Petersburg, Russian Federation
| | - Angela R Perri
- PaleoWest, Henderson, NV, USA.,Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Małgorzata Pilot
- Museum & Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
| | - Vladimir V Pitulko
- Institute for the History of Material Culture, Russian Academy of Sciences, St Petersburg, Russian Federation
| | | | | | | | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russian Federation
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR 5288, CNRS, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Jan Storå
- Stockholm University, Stockholm, Sweden
| | | | - Victor F Zaibert
- Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Grant Zazula
- Yukon Palaeontology Program, Whitehorse, Yukon Territories, Canada.,Collections and Research, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | | | - Anders J Hansen
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden.,Stockholm University, Stockholm, Sweden
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK.
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7
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Abstract
Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland;
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8
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Abstract
The predominant phylogenetic patterns within a genome do not always reflect correctly the history of evolutionary divergence and speciation, and the true phylogenetic signal tends to be concentrated within low-recombination regions of the genome. In this issue of Molecular Ecology, Hennelly et al. show that this is also the case for intraspecific relationships that are characterized by considerable gene flow between lineages. The study reconstructs the phylogenetic relationships of Indian and Tibetan wolves with other grey wolf (Canis lupus) populations worldwide, and demonstrates that these two populations represent phylogenetically distinct lineages. This inference was supported by using low-recombination regions of autosomal chromosomes and the X chromosome, which proved to be essential for correct inference of the lineage splitting order. Their study illustrates the power of analytical approaches that implement knowledge of genome evolution patterns to reconstruct complex intraspecific evolutionary relationships. The study also provides a compelling example of the application of modern phylogenomic approaches in the identification of evolutionarily significant units for the purpose of species conservation.
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Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Gdańsk, Poland
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9
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Pilot M, Moura AE, Okhlopkov IM, Mamaev NV, Manaseryan NH, Hayrapetyan V, Kopaliani N, Tsingarska E, Alagaili AN, Mohammed OB, Ostrander EA, Bogdanowicz W. Human-modified canids in human-modified landscapes: The evolutionary consequences of hybridization for grey wolves and free-ranging domestic dogs. Evol Appl 2021; 14:2433-2456. [PMID: 34745336 PMCID: PMC8549620 DOI: 10.1111/eva.13257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 05/05/2021] [Accepted: 05/19/2021] [Indexed: 12/22/2022] Open
Abstract
Introgressive hybridization between domestic animals and their wild relatives is an indirect form of human-induced evolution, altering gene pools and phenotypic traits of wild and domestic populations. Although this process is well documented in many taxa, its evolutionary consequences are poorly understood. In this study, we assess introgression patterns in admixed populations of Eurasian wolves and free-ranging domestic dogs (FRDs), identifying chromosomal regions with significantly overrepresented hybrid ancestry and assessing whether genes located within these regions show signatures of selection. Although the dog admixture proportion in West Eurasian wolves (2.7%) was greater than the wolf admixture proportion in FRDs (0.75%), the number and average length of chromosomal blocks showing significant overrepresentation of hybrid ancestry were smaller in wolves than FRDs. In wolves, 6% of genes located within these blocks showed signatures of positive selection compared to 23% in FRDs. We found that introgression from wolves may provide a considerable adaptive advantage to FRDs, counterbalancing some of the negative effects of domestication, which can include reduced genetic diversity and excessive tameness. In wolves, introgression from FRDs is mostly driven by drift, with a small number of positively selected genes associated with brain function and behaviour. The predominance of drift may be the consequence of small effective size of wolf populations, which reduces efficiency of selection for weakly advantageous or against weakly disadvantageous introgressed variants. Small wolf population sizes result largely from human-induced habitat loss and hunting, thus linking introgression rates to anthropogenic processes. Our results imply that maintenance of large population sizes should be an important element of wolf management strategies aimed at reducing introgression rates of dog-derived variants.
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Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of ZoologyPolish Academy of SciencesWarsawPoland
| | - Andre E. Moura
- Museum and Institute of ZoologyPolish Academy of SciencesWarsawPoland
| | - Innokentiy M. Okhlopkov
- Institute of Biological Problems of CryolithozoneSiberian Branch of Russian Academy of SciencesYakutskRussia
| | - Nikolay V. Mamaev
- Institute of Biological Problems of CryolithozoneSiberian Branch of Russian Academy of SciencesYakutskRussia
| | - Ninna H. Manaseryan
- Scientific Center of Zoology and HydroecologyNational Academy of SciencesYerevanArmenia
| | | | | | | | - Abdulaziz N. Alagaili
- KSU Mammals Research ChairDepartment of ZoologyKing Saud UniversityRiyadhSaudi Arabia
| | - Osama B. Mohammed
- KSU Mammals Research ChairDepartment of ZoologyKing Saud UniversityRiyadhSaudi Arabia
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
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10
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Natoli E, Bonanni R, Cafazzo S, Mills DS, Pontier D, Pilot M. Genetic inference of the mating system of free-ranging domestic dogs. Behav Ecol 2021; 32:646-656. [PMID: 34539241 PMCID: PMC8444980 DOI: 10.1093/beheco/arab011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 12/11/2020] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
Domestication has greatly changed the social and reproductive behavior of dogs relative to that of wild members of the genus Canis, which typically exhibit social monogamy and extended parental care. Unlike a typical gray wolf pack that consists of a single breeding pair and their offspring from multiple seasons, a group of free-ranging dogs (FRDs) can include multiple breeding individuals of both sexes. To understand the consequences of this shift in reproductive behavior, we reconstructed the genetic pedigree of an FRD population and assessed the kinship patterns in social groups, based on genome-wide single-nucleotide polymorphism genotypes. Consistent with behavioral observations, the mating system of the study population was characterized by polygynandry. Instead of the discreet family units observed in wolves, FRDs were linked by a network of kinship relationships that spread across packs. However, we also observed reproduction of the same male-female pairs in multiple seasons, retention of adult offspring in natal packs, and dispersal between neighboring packs-patterns in common with wolves. Although monogamy is the predominant mating system in wolves, polygyny and polyandry are occasionally observed in response to increased food availability. Thus, polygynandry of domestic dogs was likely influenced by the shift in ecological niche from an apex predator to a human commensal.
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Affiliation(s)
- Eugenia Natoli
- Canile Sovrazonale, ASL Roma 3 (Local Health Unit Rome 3), Via della Magliana 856H, 00148 Rome, Italy
| | | | | | - Daniel S Mills
- School of Life Sciences, University of Lincoln, Lincoln LN6 7DL, UK
| | - Dominique Pontier
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland
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11
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Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, Möller L, Natoli A, Gaspari S, McGowen M, Chen I, Gray H, Gore M, Culloch RM, Kiani MS, Willson MS, Bulushi A, Collins T, Baldwin R, Willson A, Minton G, Ponnampalam L, Hoelzel AR. Corrigendum to "Phylogenomics of the genus Tursiops and closely related delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers" [Mol. Phylogenet. Evol. 146 (2020) 106756]. Mol Phylogenet Evol 2021; 157:107047. [PMID: 33431184 DOI: 10.1016/j.ympev.2020.107047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Andre E Moura
- Museum and Institute of Zoology, Polish Academy of Sciences, Poland; School of Life Sciences, University of Lincoln, UK.
| | - Kypher Shreves
- School of Life Sciences, University of Lincoln, UK; Institute of Medical Sciences, School of Medical Sciences, University of Aberdeen, UK
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Poland; School of Life Sciences, University of Lincoln, UK
| | - Kimberly R Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, USA
| | | | | | - Luciana Möller
- College of Science and Engineering, Flinders University, Australia
| | - Ada Natoli
- College of Natural and Health Sciences, Zayed University, United Arab Emirates
| | - Stefania Gaspari
- Consiglio Nazionale delle Ricerche-Istituto di Scienze Marine, Ancona, Italy
| | | | - Ing Chen
- Division of Science, Yale-NUS College, Singapore
| | - Howard Gray
- School of Biosciences, Durham University, UK
| | | | - Ross M Culloch
- School of Biosciences, Durham University, UK; Marine Scotland Science, Scottish Government, Marine Laboratory, UK
| | | | | | | | - Tim Collins
- Ocean Giants Program, Wildlife Conservation Society, USA
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12
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Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, Möller L, Natoli A, Gaspari S, McGowen M, Chen I, Gray H, Gore M, Culloch RM, Kiani MS, Willson MS, Bulushi A, Collins T, Baldwin R, Willson A, Minton G, Ponnampalam L, Hoelzel AR. Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers. Mol Phylogenet Evol 2020; 146:106756. [DOI: 10.1016/j.ympev.2020.106756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/02/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022]
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13
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Pilot M, Moura AE, Okhlopkov IM, Mamaev NV, Alagaili AN, Mohammed OB, Yavruyan EG, Manaseryan NH, Hayrapetyan V, Kopaliani N, Tsingarska E, Krofel M, Skoglund P, Bogdanowicz W. Global Phylogeographic and Admixture Patterns in Grey Wolves and Genetic Legacy of An Ancient Siberian Lineage. Sci Rep 2019; 9:17328. [PMID: 31757998 PMCID: PMC6874602 DOI: 10.1038/s41598-019-53492-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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] [Received: 05/23/2019] [Accepted: 11/01/2019] [Indexed: 12/12/2022] Open
Abstract
The evolutionary relationships between extinct and extant lineages provide important insight into species' response to environmental change. The grey wolf is among the few Holarctic large carnivores that survived the Late Pleistocene megafaunal extinctions, responding to that period's profound environmental changes with loss of distinct lineages and phylogeographic shifts, and undergoing domestication. We reconstructed global genome-wide phylogeographic patterns in modern wolves, including previously underrepresented Siberian wolves, and assessed their evolutionary relationships with a previously genotyped wolf from Taimyr, Siberia, dated at 35 Kya. The inferred phylogeographic structure was affected by admixture with dogs, coyotes and golden jackals, stressing the importance of accounting for this process in phylogeographic studies. The Taimyr lineage was distinct from modern Siberian wolves and constituted a sister lineage of modern Eurasian wolves and domestic dogs, with an ambiguous position relative to North American wolves. We detected gene flow from the Taimyr lineage to Arctic dog breeds, but population clustering methods indicated closer similarity of the Taimyr wolf to modern wolves than dogs, implying complex post-divergence relationships among these lineages. Our study shows that introgression from ecologically diverse con-specific and con-generic populations was common in wolves' evolutionary history, and could have facilitated their adaptation to environmental change.
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Affiliation(s)
- Małgorzata Pilot
- School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Andre E Moura
- School of Life Sciences, University of Lincoln, Lincoln, United Kingdom
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Innokentiy M Okhlopkov
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Nikolay V Mamaev
- Institute of Biological Problems of Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk, Russia
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department of Zoology, King Saud University, Riyadh, Saudi Arabia
| | - Osama B Mohammed
- KSU Mammals Research Chair, Department of Zoology, King Saud University, Riyadh, Saudi Arabia
| | - Eduard G Yavruyan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences, Yerevan, Armenia
| | - Ninna H Manaseryan
- Scientific Center of Zoology and Hydroecology, National Academy of Sciences, Yerevan, Armenia
| | | | - Natia Kopaliani
- Institute of Ecology, Ilia State University, Tbilisi, Georgia
| | | | - Miha Krofel
- Department of Forestry, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | | | - Wiesław Bogdanowicz
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland.
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14
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Waterman JO, Campbell LAD, Maréchal L, Pilot M, Majolo B. Effect of human activity on habitat selection in the endangered Barbary macaque. Anim Conserv 2019. [DOI: 10.1111/acv.12543] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J. O. Waterman
- School of Psychology University of Lincoln Lincoln UK
- School of Natural Sciences & Psychology Liverpool John Moores University Liverpool UK
| | - L. A. D. Campbell
- School of Psychology University of Lincoln Lincoln UK
- WildCRU, Recanti‐Kaplan Centre University of Oxford Tubney UK
| | - L. Maréchal
- School of Psychology University of Lincoln Lincoln UK
| | - M. Pilot
- School of Life Sciences University of Lincoln Lincoln UK
- Museum and Institute of Zoology Polish Academy of Sciences Gdańsk Poland
| | - B. Majolo
- School of Psychology University of Lincoln Lincoln UK
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15
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Pilot M, Greco C, vonHoldt BM, Randi E, Jędrzejewski W, Sidorovich VE, Konopiński MK, Ostrander EA, Wayne RK. Widespread, long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids. Evol Appl 2018; 11:662-680. [PMID: 29875809 PMCID: PMC5978975 DOI: 10.1111/eva.12595] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 07/04/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023] Open
Abstract
Hybridisation between a domesticated species and its wild ancestor is an important conservation problem, especially if it results in the introgression of domestic gene variants into wild species. Nevertheless, the legal status of hybrids remains unregulated, partially because of the limited understanding of the hybridisation process and its consequences. The occurrence of hybridisation between grey wolves and domestic dogs is well documented from different parts of the wolf geographic range, but little is known about the frequency of hybridisation events, their causes and the genetic impact on wolf populations. We analysed 61K SNPs spanning the canid genome in wolves from across Eurasia and North America and compared that data to similar data from dogs to identify signatures of admixture. The haplotype block analysis, which included 38 autosomes and the X chromosome, indicated the presence of individuals of mixed wolf-dog ancestry in most Eurasian wolf populations, but less admixture was present in North American populations. We found evidence for male-biased introgression of dog alleles into wolf populations, but also identified a first-generation hybrid resulting from mating between a female dog and a male wolf. We found small blocks of dog ancestry in the genomes of 62% Eurasian wolves studied and melanistic individuals with no signs of recent admixed ancestry, but with a dog-derived allele at a locus linked to melanism. Consequently, these results suggest that hybridisation has been occurring in different parts of Eurasia on multiple timescales and is not solely a recent phenomenon. Nevertheless, wolf populations have maintained genetic differentiation from dogs, suggesting that hybridisation at a low frequency does not diminish distinctiveness of the wolf gene pool. However, increased hybridisation frequency may be detrimental for wolf populations, stressing the need for genetic monitoring to assess the frequency and distribution of individuals resulting from recent admixture.
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Affiliation(s)
| | - Claudia Greco
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Ettore Randi
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
- Department 18/Section of Environmental EngineeringAalborg UniversityAalborgDenmark
| | - Włodzimierz Jędrzejewski
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Present address:
Instituto Venezolano de Investigaciones Cientificas (IVIC)Centro de EcologiaCaracasVenezuela
| | | | | | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCAUSA
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16
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Pilot M, Malewski T, Moura AE, Grzybowski T, Oleński K, Ruść A, Kamiński S, Ruiz Fadel F, Mills DS, Alagaili AN, Mohammed OB, Kłys G, Okhlopkov IM, Suchecka E, Bogdanowicz W. On the origin of mongrels: evolutionary history of free-breeding dogs in Eurasia. Proc Biol Sci 2017; 282:20152189. [PMID: 26631564 DOI: 10.1098/rspb.2015.2189] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Although a large part of the global domestic dog population is free-ranging and free-breeding, knowledge of genetic diversity in these free-breeding dogs (FBDs) and their ancestry relations to pure-breed dogs is limited, and the indigenous status of FBDs in Asia is still uncertain. We analyse genome-wide SNP variability of FBDs across Eurasia, and show that they display weak genetic structure and are genetically distinct from pure-breed dogs rather than constituting an admixture of breeds. Our results suggest that modern European breeds originated locally from European FBDs. East Asian and Arctic breeds show closest affinity to East Asian FBDs, and they both represent the earliest branching lineages in the phylogeny of extant Eurasian dogs. Our biogeographic reconstruction of ancestral distributions indicates a gradual westward expansion of East Asian indigenous dogs to the Middle East and Europe through Central and West Asia, providing evidence for a major expansion that shaped the patterns of genetic differentiation in modern dogs. This expansion was probably secondary and could have led to the replacement of earlier resident populations in Western Eurasia. This could explain why earlier studies based on modern DNA suggest East Asia as the region of dog origin, while ancient DNA and archaeological data point to Western Eurasia.
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Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland School of Life Sciences, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
| | - Tadeusz Malewski
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland
| | - Andre E Moura
- School of Life Sciences, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
| | - Tomasz Grzybowski
- Division of Molecular and Forensic Genetics, Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University, Skłodowskiej-Curie 9, Bydgoszcz 85-094, Poland
| | - Kamil Oleński
- Department of Animal Genetics, University of Warmia and Mazury, Oczapowskiego 5, Olsztyn 10-711, Poland
| | - Anna Ruść
- Department of Animal Genetics, University of Warmia and Mazury, Oczapowskiego 5, Olsztyn 10-711, Poland
| | - Stanisław Kamiński
- Department of Animal Genetics, University of Warmia and Mazury, Oczapowskiego 5, Olsztyn 10-711, Poland
| | - Fernanda Ruiz Fadel
- School of Life Sciences, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
| | - Daniel S Mills
- School of Life Sciences, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
| | - Abdulaziz N Alagaili
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Osama B Mohammed
- KSU Mammals Research Chair, Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Grzegorz Kłys
- Department of Biosystematics, University of Opole, Oleska 22, Opole 45-052, Poland
| | - Innokentiy M Okhlopkov
- Science Institute of Biological Problems Cryolithozone, Siberian Branch of Russian Academy of Sciences, Yakutsk 677980, Russia
| | - Ewa Suchecka
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland
| | - Wiesław Bogdanowicz
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, Warszawa 00-679, Poland
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17
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Park S, Pilot M, Alexander M, Rosengart A. P-008 Evaluating Racial/Ethnic Disparity in Endovascular Thrombectomy Outcome for Acute Stroke Patients: 4,763 patients using Premier data 2011 to 2015. J Neurointerv Surg 2016. [DOI: 10.1136/neurintsurg-2016-012589.50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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18
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de Groot GA, Nowak C, Skrbinšek T, Andersen LW, Aspi J, Fumagalli L, Godinho R, Harms V, Jansman HA, Liberg O, Marucco F, Mysłajek RW, Nowak S, Pilot M, Randi E, Reinhardt I, Śmietana W, Szewczyk M, Taberlet P, Vilà C, Muñoz-Fuentes V. Decades of population genetic research reveal the need for harmonization of molecular markers: the grey wolf C
anis lupus
as a case study. Mamm Rev 2015. [DOI: 10.1111/mam.12052] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- G. Arjen de Groot
- Animal Ecology; Alterra, Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - Carsten Nowak
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
| | - Tomaž Skrbinšek
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Večna pot 111 Ljubljana 1000 Slovenia
| | | | - Jouni Aspi
- Department of Biology, Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Luca Fumagalli
- Department of Ecology and Evolution; Laboratory for Conservation Biology; Biophore Building; University of Lausanne; 1015 Lausanne Switzerland
| | - Raquel Godinho
- Research Center in Biodiversity and Genetic Resources; CIBIO/InBio; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Department of Biology; Faculty of Sciences; University of Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Department of Zoology; Faculty of Sciences; University of Johannesburg; Auckland Park 2006 Johannesburg South Africa
| | - Verena Harms
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
| | - Hugh A.H. Jansman
- Animal Ecology; Alterra, Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - Olof Liberg
- Swedish University of Agricultural Sciences (SLU); Grimsö Wildlife Research Station SE-730 91 Riddarhyttan Sweden
| | - Francesca Marucco
- Parco Naturale Alpi Marittime; Centro Gestione e Conservazione Grandi Carnivori; Piazza Regina Elena 30 12010 Valdieri Italy
| | - Robert W. Mysłajek
- Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawińskiego 5a 02-106 Warszawa Poland
| | - Sabina Nowak
- Association for Nature ‘Wolf’; Twardorzeczka 229 34-324 Lipowa Poland
| | - Małgorzata Pilot
- School of Life Sciences; University of Lincoln; Green Lane Lincoln LN6 7DL UK
| | - Ettore Randi
- Laboratorio di Genetica; Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA); Via Cà Fornacetta 9 40064 Ozzano dell'Emilia (BO) Italy
- Aalborg University; Department 18/Section of Environmental Engineering; Sohngårdsholmsvej 57 9000 Aalborg Denmark
| | - Ilka Reinhardt
- LUPUS - German Institute for Wolf Monitoring and Research; Dorfstraße 20 02979 Spreewitz Germany
| | - Wojciech Śmietana
- Polish Academy of Sciences; Institute of Nature Conservation; Mickiewicza 33 31-120 Kraków Poland
| | - Maciej Szewczyk
- Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawińskiego 5a 02-106 Warszawa Poland
| | - Pierre Taberlet
- Centre National de la Recherche Scientifique; Laboratoire d'Ecologie Alpine (LECA); F-38000 Grenoble France
- Université Grenoble Alpes; Laboratoire d'Ecologie Alpine (LECA); F-38000 Grenoble France
| | - Carles Vilà
- Doñana Biological Station (EBD-CSIC); Avenida Americo Vespucio s/n 41092 Sevilla Spain
| | - Violeta Muñoz-Fuentes
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
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19
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Pilot M, Greco C, vonHoldt BM, Jędrzejewska B, Randi E, Jędrzejewski W, Sidorovich VE, Ostrander EA, Wayne RK. Genome-wide signatures of population bottlenecks and diversifying selection in European wolves. Heredity (Edinb) 2013; 112:428-42. [PMID: 24346500 DOI: 10.1038/hdy.2013.122] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 10/14/2013] [Accepted: 10/16/2013] [Indexed: 12/21/2022] Open
Abstract
Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability.
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Affiliation(s)
- M Pilot
- 1] School of Life Sciences, University of Lincoln, Lincoln, UK [2] Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - C Greco
- Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Rome and Ozzano Emilia (BO), Italy
| | - B M vonHoldt
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - B Jędrzejewska
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - E Randi
- 1] Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Rome and Ozzano Emilia (BO), Italy [2] Aalborg University, Department 18, Section of Environmental Engineering, Aalborg, Denmark
| | - W Jędrzejewski
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - V E Sidorovich
- Institute of Zoology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - E A Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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Dąbrowski MJ, Pilot M, Kruczyk M, Żmihorski M, Umer HM, Gliwicz J. Reliability assessment of null allele detection: inconsistencies between and within different methods. Mol Ecol Resour 2013; 14:361-73. [PMID: 24119056 DOI: 10.1111/1755-0998.12177] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [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: 01/30/2012] [Revised: 09/17/2013] [Accepted: 09/20/2013] [Indexed: 11/29/2022]
Abstract
Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8 years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false-positive and false-negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false-positive rate, but this approach may increase the false-negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural populations.
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Affiliation(s)
- M J Dąbrowski
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warsaw, Poland; Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24, Uppsala, Sweden
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Stronen AV, Jędrzejewska B, Pertoldi C, Demontis D, Randi E, Niedziałkowska M, Pilot M, Sidorovich VE, Dykyy I, Kusak J, Tsingarska E, Kojola I, Karamanlidis AA, Ornicans A, Lobkov VA, Dumenko V, Czarnomska SD. North-South differentiation and a region of high diversity in European wolves (Canis lupus). PLoS One 2013; 8:e76454. [PMID: 24146871 PMCID: PMC3795770 DOI: 10.1371/journal.pone.0076454] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [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: 01/26/2013] [Accepted: 08/23/2013] [Indexed: 11/18/2022] Open
Abstract
European wolves (Canis lupus) show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP) loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan) differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan) in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part.
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Affiliation(s)
- Astrid V. Stronen
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
- * E-mail:
| | | | - Cino Pertoldi
- Department of Biosciences, Aarhus University, Aarhus, Denmark
- Aalborg University, Department 18/Section of Environmental Engineering, Aalborg, Denmark
- Aalborg Zoo, Aalborg, Denmark
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ettore Randi
- Aalborg University, Department 18/Section of Environmental Engineering, Aalborg, Denmark
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale, Ozzano Emilia (BO), Italy
| | | | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warszawa, Poland
| | - Vadim E. Sidorovich
- Institute of Zoology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Ihor Dykyy
- Department of Zoology, Biological Faculty, Ivan Franko National University of Lviv, Lviv, Ukraine
| | - Josip Kusak
- Department of Biology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Ilpo Kojola
- Finnish Game and Fisheries Research Institute, Oulu, Finland
| | - Alexandros A. Karamanlidis
- ARCTUROS, Civil Society for the Protection and Management of Wildlife and the Natural Environment, Thessaloniki, Greece
- Department of Ecology and Natural Resources Management, Norwegian University of Life Sciences, Ås, Norway
| | - Aivars Ornicans
- Latvian State Forest Research Institute “Silava”, Salaspils, Latvia
| | - Vladimir A. Lobkov
- Zoological museum of Odessa, National I.I. Mechnikov University, Odessa, Ukraine
| | - Vitalii Dumenko
- Biosphere Reserve Askania Nova, Askania-Nova, Chaplynka District, Kherson Region, Ukraine
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Czarnomska SD, Jędrzejewska B, Borowik T, Niedziałkowska M, Stronen AV, Nowak S, Mysłajek RW, Okarma H, Konopiński M, Pilot M, Śmietana W, Caniglia R, Fabbri E, Randi E, Pertoldi C, Jędrzejewski W. Concordant mitochondrial and microsatellite DNA structuring between Polish lowland and Carpathian Mountain wolves. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0446-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Pilot M, Jędrzejewski W, Sidorovich VE, Meier-Augenstein W, Hoelzel AR. Dietary differentiation and the evolution of population genetic structure in a highly mobile carnivore. PLoS One 2012; 7:e39341. [PMID: 22768075 PMCID: PMC3387138 DOI: 10.1371/journal.pone.0039341] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [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: 11/28/2011] [Accepted: 05/18/2012] [Indexed: 11/18/2022] Open
Abstract
Recent studies on highly mobile carnivores revealed cryptic population genetic structures correlated to transitions in habitat types and prey species composition. This led to the hypothesis that natal-habitat-biased dispersal may be responsible for generating population genetic structure. However, direct evidence for the concordant ecological and genetic differentiation between populations of highly mobile mammals is rare. To address this we analyzed stable isotope profiles (δ13C and δ15N values) for Eastern European wolves (Canis lupus) as a quantifiable proxy measure of diet for individuals that had been genotyped in an earlier study (showing cryptic genetic structure), to provide a quantitative assessment of the relationship between individual foraging behavior and genotype. We found a significant correlation between genetic distances and dietary differentiation (explaining 46% of the variation) in both the marginal test and crucially, when geographic distance was accounted for as a co-variable. These results, interpreted in the context of other possible mechanisms such as allopatry and isolation by distance, reinforce earlier studies suggesting that diet and associated habitat choice are influencing the structuring of populations in highly mobile carnivores.
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Affiliation(s)
- Małgorzata Pilot
- School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom
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Kalka D, Domagala Z, Wojcieszczyk J, Rusiecki L, Koleda P, Kowalewski P, Pilot M, Grychowski A, Rusiecka M, Pilecki W. 122 HEALTH-ORIENTED PHYSICAL ACTIVITY IN MOULDING PHYSICAL EFFICIENCY OF WOMEN TREATED INVASIVELY DUE TO ISCHEMIC HEART DISEASE. Maturitas 2012. [DOI: 10.1016/s0378-5122(12)70233-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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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Pilot M, Dabrowski MJ, Jancewicz E, Schtickzelle N, Gliwicz J. Temporally stable genetic variability and dynamic kinship structure in a fluctuating population of the root vole Microtus oeconomus. Mol Ecol 2010; 19:2800-12. [PMID: 20561198 DOI: 10.1111/j.1365-294x.2010.04692.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [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 variability, kin structure and demography of a population are mutually dependent. Population genetic theory predicts that under demographically stable conditions, neutral genetic variability reaches equilibrium between gene flow and drift. However, density fluctuations and non-random mating, resulting e.g. from kin clustering, may lead to changes in genetic composition over time. Theoretical models also predict that changes in kin structure may affect aggression level and recruitment, leading to density fluctuations. These predictions have been rarely tested in natural populations. The aim of this study was to analyse changes in genetic variability and kin structure in a local population of the root vole (Microtus oeconomus) that underwent a fourfold change in mean density over a 6-year period. Intensive live-trapping resulted in sampling 88% of individuals present in the study area, as estimated from mark-recapture data. Based on 642 individual genotypes at 20 microsatellite loci, we compared genetic variability and kin structure of this population between consecutive years. We found that immigration was negatively correlated with density, while the number of kin groups was positively correlated with density. This is consistent with theoretical predictions that changes in kin structure play an important role in population fluctuations. Despite the changes in density and kin structure, there was no genetic differentiation between years. Population-level genetic diversity measures did not significantly vary in time and remained relatively high (H(E) range: 0.72-0.78). These results show that a population that undergoes significant demographic and social changes may maintain high genetic variability and stable genetic composition.
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Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland.
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Pilot M, Branicki W, Jedrzejewski W, Goszczyński J, Jedrzejewska B, Dykyy I, Shkvyrya M, Tsingarska E. Phylogeographic history of grey wolves in Europe. BMC Evol Biol 2010; 10:104. [PMID: 20409299 PMCID: PMC2873414 DOI: 10.1186/1471-2148-10-104] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [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: 05/05/2009] [Accepted: 04/21/2010] [Indexed: 02/06/2023] Open
Abstract
Background While it is generally accepted that patterns of intra-specific genetic differentiation are substantially affected by glacial history, population genetic processes occurring during Pleistocene glaciations are still poorly understood. In this study, we address the question of the genetic consequences of Pleistocene glaciations for European grey wolves. Combining our data with data from published studies, we analysed phylogenetic relationships and geographic distribution of mitochondrial DNA haplotypes for 947 contemporary European wolves. We also compared the contemporary wolf sequences with published sequences of 24 ancient European wolves. Results We found that haplotypes representing two haplogroups, 1 and 2, overlap geographically, but substantially differ in frequency between populations from south-western and eastern Europe. A comparison between haplotypes from Europe and other continents showed that both haplogroups are spread throughout Eurasia, while only haplogroup 1 occurs in contemporary North American wolves. All ancient wolf samples from western Europe that dated from between 44,000 and 1,200 years B.P. belonged to haplogroup 2, suggesting the long-term predominance of this haplogroup in this region. Moreover, a comparison of current and past frequencies and distributions of the two haplogroups in Europe suggested that haplogroup 2 became outnumbered by haplogroup 1 during the last several thousand years. Conclusions Parallel haplogroup replacement, with haplogroup 2 being totally replaced by haplogroup 1, has been reported for North American grey wolves. Taking into account the similarity of diets reported for the late Pleistocene wolves from Europe and North America, the correspondence between these haplogroup frequency changes may suggest that they were associated with ecological changes occurring after the Last Glacial Maximum.
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Affiliation(s)
- Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 00-679 Warszawa, Poland.
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Pilot M, Dahlheim ME, Hoelzel AR. Social cohesion among kin, gene flow without dispersal and the evolution of population genetic structure in the killer whale (Orcinus orca). J Evol Biol 2009; 23:20-31. [PMID: 19912451 DOI: 10.1111/j.1420-9101.2009.01887.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In social species, breeding system and gregarious behavior are key factors influencing the evolution of large-scale population genetic structure. The killer whale is a highly social apex predator showing genetic differentiation in sympatry between populations of foraging specialists (ecotypes), and low levels of genetic diversity overall. Our comparative assessments of kinship, parentage and dispersal reveal high levels of kinship within local populations and ongoing male-mediated gene flow among them, including among ecotypes that are maximally divergent within the mtDNA phylogeny. Dispersal from natal populations was rare, implying that gene flow occurs without dispersal, as a result of reproduction during temporary interactions. Discordance between nuclear and mitochondrial phylogenies was consistent with earlier studies suggesting a stochastic basis for the magnitude of mtDNA differentiation between matrilines. Taken together our results show how the killer whale breeding system, coupled with social, dispersal and foraging behaviour, contributes to the evolution of population genetic structure.
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Affiliation(s)
- M Pilot
- School of Biological and Biomedical Sciences, University of Durham, Durham, UK
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Pilot M, Gralak B, Goszczyński J, Posłuszny M. A method of genetic identification of pine marten (Martes martes) and stone marten (Martes foina) and its application to faecal samples. J Zool (1987) 2007. [DOI: 10.1111/j.1469-7998.2006.00179.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [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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Goszczyński J, Posłuszny M, Pilot M, Gralak B. Patterns of winter locomotion and foraging in two sympatric marten species: Martes martes and Martes foina. CAN J ZOOL 2007. [DOI: 10.1139/z06-212] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Modes of area searching and exploratory behaviour of the sympatric pine marten, Martes martes (L., 1758), and stone marten, Martes foina (Erxleben, 1777), were studied by snow-tracking in two regions of Poland. The accuracy of identifications of the two species on the basis of their snow tracks was assessed by DNA analysis of their faeces, as collected on the tracks; identifications were found to be correct in 88% of cases. Although most activities of the two species were concentrated on the forest floor, pine martens climbed trees, moved in tree crowns, and searched the bases of tree trunks and tree hollows more frequently than stone martens. In contrast, stone martens were more inclined to search for food in brushwood and piles of wood, and visited logged areas and garbage dumps more frequently. Pine martens avoided man-made objects and barriers such as roads and passed through open areas with reluctance. Such behavioural traits make this species particularly vulnerable to forest fragmentation and human activity in forests. Stone martens often explored woodless areas and inhabited buildings, which allowed them to use habitats substantially transformed and intensively explored by humans. The future coexistence and relative numbers of the two martens in forest habitats will depend on the mode of forest management and on the existence of effective migratory corridors connecting forest patches.
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Affiliation(s)
- Jacek Goszczyński
- Museum and Institute of Zoology, Polish Academy of Sciences, ulica Wilcza 64, 00-679 Warsaw, Poland
- Department of Forest Protection and Ecology, Warsaw Agricultural University, ulica Nowoursynowska 159, 02-776 Warsaw, Poland
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, 05-552 Wólka Kosowska, Poland
| | - Maciej Posłuszny
- Museum and Institute of Zoology, Polish Academy of Sciences, ulica Wilcza 64, 00-679 Warsaw, Poland
- Department of Forest Protection and Ecology, Warsaw Agricultural University, ulica Nowoursynowska 159, 02-776 Warsaw, Poland
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, 05-552 Wólka Kosowska, Poland
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ulica Wilcza 64, 00-679 Warsaw, Poland
- Department of Forest Protection and Ecology, Warsaw Agricultural University, ulica Nowoursynowska 159, 02-776 Warsaw, Poland
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, 05-552 Wólka Kosowska, Poland
| | - Barbara Gralak
- Museum and Institute of Zoology, Polish Academy of Sciences, ulica Wilcza 64, 00-679 Warsaw, Poland
- Department of Forest Protection and Ecology, Warsaw Agricultural University, ulica Nowoursynowska 159, 02-776 Warsaw, Poland
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, 05-552 Wólka Kosowska, Poland
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Qin X, Pilot M, Thompson H, Maskell J. Effects of spiramycin on gastrointestinal motility. Chemioterapia 1987; 6:319-20. [PMID: 3509431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- X Qin
- Microbiology Department, London Hospital Medical College, England
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Abstract
The duodenal transmural potential difference (pd) has been studied in isolated vascular-perfused preparations of canine stomach and duodenum. There was no quantitative correlation between the magnitude of the intraluminal pressure change and pd but fluctuations of pd in these preparations were related to duodenal slow wave activity.
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