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Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Author Correction: Universal DNA methylation age across mammalian tissues. Nat Aging 2023; 3:1462. [PMID: 37674040 PMCID: PMC10645586 DOI: 10.1038/s43587-023-00499-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Affiliation(s)
- A T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - Z Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | - A Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - T R Robeck
- Zoological SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - J A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - R Lowe
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Q Yan
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - J Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - H Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - V A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - J Almunia
- Loro Parque Fundacion, Puerto de la Cruz, Spain
| | - A Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - R Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C S Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - G Banks
- School of Science and Technology, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - K Belov
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - N C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - P Black
- Busch Gardens Tampa, Tampa, FL, USA
| | - D T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - E K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - C E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - R T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - J L Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - G G Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - A Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J M Cavin
- Gulf World, Dolphin Company, Panama City Beach, FL, USA
| | - L Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - H Chen
- Department of Pharmacology, Addiction Science and Toxicology, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - O W Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - L N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - M L Cossette
- Department of Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - J Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - J DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S DiRocco
- SeaWorld of Florida, Orlando, FL, USA
| | - C Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | | | - C K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - S Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E Erbay
- Altos Labs, San Francisco, CA, USA
| | - C Erlacher-Reid
- SeaWorld of Florida, Orlando, FL, USA
- SeaWorld Orlando, Orlando, FL, USA
| | - C G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - S H Ferguson
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - J M Gaillard
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - E Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - L Gerber
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - V N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - R G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - M J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - C B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - D W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - M Haulena
- Vancouver Aquarium, Vancouver, British Columbia, Canada
| | - K Herrick
- SeaWorld of California, San Diego, CA, USA
| | - A N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C J Hogg
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - T A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - T Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
- Division of Genetics and Metabolism, Oishei Children's Hospital, Buffalo, NY, USA
| | | | - A J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - G Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - O Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - H Katcher
- Yuvan Research, Mountain View, CA, USA
| | | | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - H Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Kordowitzki
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn, Poland
- Institute for Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | - W R Koski
- LGL Limited, King City, Ontario, Canada
| | - M Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - S B Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Center for Tropical Research, Institute for the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - S G Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - J F Lemaitre
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - A J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - X Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - D T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - T J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - N Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - D Maddox
- White Oak Conservation, Yulee, FL, USA
| | - C O Matkin
- North Gulf Oceanic Society, Homer, AK, USA
| | - J A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - J Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - J J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - G A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - K Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - J Munshi-South
- Louis Calder Center-Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M Nagy
- Museum fur Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - P Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - P W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - N B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Niehrs
- Institute of Molecular Biology, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - J K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - P O'Tierney Ginn
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - D T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - A G Ophir
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - S Osborn
- SeaWorld of Texas, San Antonio, TX, USA
| | - E A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - K M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - K C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - K J Peters
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - A B Pedersen
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - D W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - G M Pinho
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
| | - P Reddy
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - B Rey
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - B R Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - J Robbins
- Center for Coastal Studies, Provincetown, MA, USA
| | | | - J Russell
- SeaWorld of California, San Diego, CA, USA
| | - E Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - L L Sailer
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - A B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - K M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | - T Schmitt
- SeaWorld of California, San Diego, CA, USA
| | | | - L B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - K E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - A W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - A Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - A B A Shafer
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - D Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - A V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - K Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - I Sinha
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - R G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - E Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | - L Staggs
- SeaWorld of Florida, Orlando, FL, USA
| | | | - K J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - D T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | - V J Sugrue
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - B Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - J S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M J Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Van Bonn
- John G. Shedd Aquarium, Chicago, IL, USA
| | - S C Vernes
- School of Biology, the University of St Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - D Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - H V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Division of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - N Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
| | - C K Williams
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - X W Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Yao
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - B G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - B Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - P Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Y Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - W Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Zimmermann
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Koblenz, Germany
| | - J Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - K Raj
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - S Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
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Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Universal DNA methylation age across mammalian tissues. Nat Aging 2023; 3:1144-1166. [PMID: 37563227 PMCID: PMC10501909 DOI: 10.1038/s43587-023-00462-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.
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Affiliation(s)
- A T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - Z Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | - A Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - T R Robeck
- Zoological SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - J A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - R Lowe
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Q Yan
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - J Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - H Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - V A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - J Almunia
- Loro Parque Fundacion, Puerto de la Cruz, Spain
| | - A Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - R Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C S Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - G Banks
- School of Science and Technology, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - K Belov
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - N C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - P Black
- Busch Gardens Tampa, Tampa, FL, USA
| | - D T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - E K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - C E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - R T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - J L Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - G G Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - A Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J M Cavin
- Gulf World, Dolphin Company, Panama City Beach, FL, USA
| | - L Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - H Chen
- Department of Pharmacology, Addiction Science and Toxicology, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - O W Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - L N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - M L Cossette
- Department of Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - J Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - J DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S DiRocco
- SeaWorld of Florida, Orlando, FL, USA
| | - C Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | | | - C K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - S Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E Erbay
- Altos Labs, San Francisco, CA, USA
| | - C Erlacher-Reid
- SeaWorld of Florida, Orlando, FL, USA
- SeaWorld Orlando, Orlando, FL, USA
| | - C G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - S H Ferguson
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - J M Gaillard
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - E Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - L Gerber
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - V N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - R G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - M J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - C B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - D W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - M Haulena
- Vancouver Aquarium, Vancouver, British Columbia, Canada
| | - K Herrick
- SeaWorld of California, San Diego, CA, USA
| | - A N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C J Hogg
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - T A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - T Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
- Division of Genetics and Metabolism, Oishei Children's Hospital, Buffalo, NY, USA
| | | | - A J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - G Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - O Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - H Katcher
- Yuvan Research, Mountain View, CA, USA
| | | | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - H Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Kordowitzki
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn, Poland
- Institute for Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | - W R Koski
- LGL Limited, King City, Ontario, Canada
| | - M Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - S B Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Center for Tropical Research, Institute for the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - S G Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - J F Lemaitre
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - A J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - X Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - D T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - T J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - N Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - D Maddox
- White Oak Conservation, Yulee, FL, USA
| | - C O Matkin
- North Gulf Oceanic Society, Homer, AK, USA
| | - J A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - J Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - J J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - G A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - K Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - J Munshi-South
- Louis Calder Center-Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M Nagy
- Museum fur Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - P Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - P W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - N B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Niehrs
- Institute of Molecular Biology, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - J K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - P O'Tierney Ginn
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - D T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - A G Ophir
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - S Osborn
- SeaWorld of Texas, San Antonio, TX, USA
| | - E A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - K M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - K C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - K J Peters
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - A B Pedersen
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - D W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - G M Pinho
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
| | - P Reddy
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - B Rey
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - B R Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - J Robbins
- Center for Coastal Studies, Provincetown, MA, USA
| | | | - J Russell
- SeaWorld of California, San Diego, CA, USA
| | - E Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - L L Sailer
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - A B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - K M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | - T Schmitt
- SeaWorld of California, San Diego, CA, USA
| | | | - L B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - K E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - A W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - A Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - A B A Shafer
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - D Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - A V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - K Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - I Sinha
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - R G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - E Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | - L Staggs
- SeaWorld of Florida, Orlando, FL, USA
| | | | - K J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - D T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | - V J Sugrue
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - B Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - J S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M J Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Van Bonn
- John G. Shedd Aquarium, Chicago, IL, USA
| | - S C Vernes
- School of Biology, the University of St Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - D Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - H V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Division of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - N Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
| | - C K Williams
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - X W Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Yao
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - B G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - B Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - P Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Y Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - W Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Zimmermann
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Koblenz, Germany
| | - J Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - K Raj
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - S Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
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Serieys LEK, Armenta TC, Moriarty JG, Boydston EE, Lyren LM, Poppenga RH, Crooks KR, Wayne RK, Riley SPD. Anticoagulant rodenticides in urban bobcats: exposure, risk factors and potential effects based on a 16-year study. Ecotoxicology 2015; 24:844-862. [PMID: 25707484 DOI: 10.1007/s10646-015-1429-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Anticoagulant rodenticides (ARs) are increasingly recognized as a threat to nontarget wildlife. High exposure to ARs has been documented globally in nontarget predatory species and linked to the high prevalence of an ectoparasitic disease, notoedric mange. In southern California, mange associated with AR exposure has been the proximate cause of a bobcat (Lynx rufus) population decline. We measured AR exposure in bobcats from two areas in southern California, examining seasonal, demographic and spatial risk factors across landscapes including natural and urbanized areas. The long-term study included bobcats sampled over a 16-year period (1997-2012) and a wide geographic area. We sampled blood (N = 206) and liver (N = 172) to examine exposure ante- and post-mortem. We detected high exposure prevalence (89 %, liver; 39 %, blood) and for individuals with paired liver and blood data (N = 64), 92 % were exposed. Moreover, the animals with the most complete sampling were exposed most frequently to three or more compounds. Toxicant exposure was associated with commercial, residential, and agricultural development. Bobcats of both sexes and age classes were found to be at high risk of exposure, and we documented fetal transfer of multiple ARs. We found a strong association between certain levels of exposure (ppm), and between multiple AR exposure events, and notoedric mange. AR exposure was prevalent throughout both regions sampled and throughout the 16-year time period in the long-term study. ARs pose a substantial threat to bobcats, and likely other mammalian and avian predators, living at the urban-wildland interface.
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Affiliation(s)
- L E K Serieys
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA,
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4
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Price SL, Powell S, Kronauer DJC, Tran LAP, Pierce NE, Wayne RK. Renewed diversification is associated with new ecological opportunity in the Neotropical turtle ants. J Evol Biol 2014; 27:242-58. [PMID: 24417316 DOI: 10.1111/jeb.12300] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [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: 07/19/2013] [Accepted: 11/12/2013] [Indexed: 01/03/2023]
Abstract
Ecological opportunity, defined as access to new resources free from competitors, is thought to be a catalyst for the process of adaptive radiation. Much of what we know about ecological opportunity, and the larger process of adaptive radiation, is derived from vertebrate diversification on islands. Here, we examine lineage diversification in the turtle ants (Cephalotes), a species-rich group of ants that has diversified throughout the Neotropics. We show that crown group turtle ants originated during the Eocene (around 46 mya), coincident with global warming and the origin of many other clades. We also show a marked lineage-wide slowdown in diversification rates in the Miocene. Contrasting this overall pattern, a species group associated with the young and seasonally harsh Chacoan biogeographic region underwent a recent burst of diversification. Subsequent analyses also indicated that there is significant phylogenetic clustering within the Chacoan region and that speciation rates are highest there. Together, these findings suggest that recent ecological opportunity, from successful colonization of novel habitat, may have facilitated renewed turtle ant diversification. Our findings highlight a central role of ecological opportunity within a successful continental radiation.
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Affiliation(s)
- S L Price
- Department of Biological Sciences, George Washington University, Washington, DC, USA; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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5
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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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Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpre MB, Sablin MV, Lopez-Giraldez F, Domingo-Roura X, Napierala H, Uerpmann HP, Loponte DM, Acosta AA, Giemsch L, Schmitz RW, Worthington B, Buikstra JE, Druzhkova A, Graphodatsky AS, Ovodov ND, Wahlberg N, Freedman AH, Schweizer RM, Koepfli KP, Leonard JA, Meyer M, Krause J, Paabo S, Green RE, Wayne RK. Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs. Science 2013; 342:871-4. [DOI: 10.1126/science.1243650] [Citation(s) in RCA: 348] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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7
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Marsden CD, Verberkmoes H, Thomas R, Wayne RK, Mable BK. Pedigrees, MHC and microsatellites: an integrated approach for genetic management of captive African wild dogs (Lycaon pictus). CONSERV GENET 2013. [DOI: 10.1007/s10592-012-0440-0] [Citation(s) in RCA: 15] [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: 11/24/2022]
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8
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Abstract
Obtaining information on wild mammal populations has been a long-standing logistical problem. However, an array of non-invasive techniques is available, including recently developed molecular genetic techniques for the analysis of feces (molecular scatology). A battery of non-invasive, molecular approaches can be used on feces, which in conjunction with conventional analysis are potentially useful for assesing genetic structure, demography and life history of mammals. Several technical problems reman before large-scale studies of feces can be undertaken productively, but already studies are providing insight into population subdivision, food habits, reproduction, sex ratio and parasitology of free-ranging populations.
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Affiliation(s)
- M H Kohn
- The Dept of Biology, University of California, 621 Circle Drive South, Los Angeles, CA 90095-1606, USA
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9
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MacDonald GM, Beilman DW, Kuzmin YV, Orlova LA, Kremenetski KV, Shapiro B, Wayne RK, Van Valkenburgh B. Pattern of extinction of the woolly mammoth in Beringia. Nat Commun 2012; 3:893. [PMID: 22692536 PMCID: PMC3621396 DOI: 10.1038/ncomms1881] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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: 12/12/2011] [Accepted: 05/02/2012] [Indexed: 11/19/2022] Open
Abstract
Extinction of the woolly mammoth in Beringia has long been subject to research and speculation. Here we use a new geo-referenced database of radiocarbon-dated evidence to show that mammoths were abundant in the open-habitat of Marine Isotope Stage 3 (∼45–30 ka). During the Last Glacial Maximum (∼25–20 ka), northern populations declined while those in interior Siberia increased. Northern mammoths increased after the glacial maximum, but declined at and after the Younger Dryas (∼12.9–11.5 ka). Remaining continental mammoths, now concentrated in the north, disappeared in the early Holocene with development of extensive peatlands, wet tundra, birch shrubland and coniferous forest. Long sympatry in Siberia suggests that humans may be best seen as a synergistic cofactor in that extirpation. The extinction of island populations occurred at ∼4 ka. Mammoth extinction was not due to a single cause, but followed a long trajectory in concert with changes in climate, habitat and human presence. Beringian mammoths were abundant 45,000 to 30,000 years ago, but then experienced a long decline in concert with changes in climate, habitat and human presence. This study uses 14C dating to trace their spatio temporal pattern of extinction until the loss of final island populations about 4,000 years ago.
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Affiliation(s)
- G M MacDonald
- UCLA, Department of Geography, UCLA, Los Angeles, California 90095-1524, USA.
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10
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Coulson T, MacNulty DR, Stahler DR, vonHoldt B, Wayne RK, Smith DW. Modeling Effects of Environmental Change on Wolf Population Dynamics, Trait Evolution, and Life History. Science 2011; 334:1275-8. [DOI: 10.1126/science.1209441] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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11
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Smith TB, Calsbeek R, Wayne RK, Holder KH, Pires D, Bardeleben C. Testing alternative mechanisms of evolutionary divergence in an African rain forest passerine bird. J Evol Biol 2005; 18:257-68. [PMID: 15715832 DOI: 10.1111/j.1420-9101.2004.00825.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [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: 11/29/2022]
Abstract
Abstract Models of speciation in African rain forests have stressed either the role of isolation or ecological gradients. Here we contrast patterns of morphological and genetic divergence in parapatric and allopatric populations of the Little Greenbul, Andropadus virens, within different and similar habitats. We sampled 263 individuals from 18 sites and four different habitat types in Upper and Lower Guinea. We show that despite relatively high rates of gene flow among populations, A. virens has undergone significant morphological divergence across the savanna-forest ecotone and mountain-forest boundaries. These data support a central component of the divergence-with-gene-flow model of speciation by suggesting that despite large amounts of gene flow, selection is sufficiently intense to cause morphological divergence. Despite evidence of isolation based on neutral genetic markers, we find little evidence of morphological divergence in fitness-related traits between hypothesized refugial areas. Although genetic evidence suggests populations in Upper and Lower Guinea have been isolated for over 2 million years, morphological divergence appears to be driven more by habitat differences than geographic isolation and suggests that selection in parapatry may be more important than geographic isolation in causing adaptive divergence in morphology.
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Affiliation(s)
- T B Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-1496, USA.
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12
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13
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Domingo-Roura X, Macdonald DW, Roy MS, Marmi J, Terradas J, Woodroffe R, Burke T, Wayne RK. Confirmation of low genetic diversity and multiple breeding females in a social group of Eurasian badgers from microsatellite and field data. Mol Ecol 2003; 12:533-9. [PMID: 12535103 DOI: 10.1046/j.1365-294x.2003.01707.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [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: 11/20/2022]
Abstract
The Eurasian badger (Meles meles) is a facultatively social carnivore that shows only rudimentary co-operative behaviour and a poorly defined social hierarchy. Behavioural evidence and limited genetic data have suggested that more than one female may breed in a social group. We combine pregnancy detection by ultrasound and microsatellite locus scores from a well-studied badger population from Wytham Woods, Oxfordshire, UK, to demonstrate that multiple females reproduce within a social group. We found that at least three of seven potential mothers reproduced in a group that contained 11 reproductive age females and nine offspring. Twelve primers showed variability across the species range and only five of these were variable in Wytham. The microsatellites showed a reduced repeat number, a significantly higher number of nonperfect repeats, and moderate heterozygosity levels in Wytham. The high frequency of imperfect repeats and demographic phenomena might be responsible for the reduced levels of variability observed in the badger.
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Affiliation(s)
- X Domingo-Roura
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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14
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Pelton MR, Gittleman JL, Funk SM, Macdonald D, Wayne RK. Carnivore Conservation. J Wildl Manage 2003. [DOI: 10.2307/3803078] [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: 11/10/2022]
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15
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Torres E, Lees DC, Vane-Wright RI, Kremen C, Leonard JA, Wayne RK. Examining monophyly in a large radiation of Madagascan butterflies (Lepidoptera: Satyrinae: Mycalesina) based on mitochondrial DNA data. Mol Phylogenet Evol 2001; 20:460-73. [PMID: 11527471 DOI: 10.1006/mpev.2001.0984] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [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: 11/22/2022]
Abstract
The satyrine butterfly subtribe Mycalesina has undergone one of the more spectacular evolutionary radiations of butterflies in the Old World tropics. Perhaps the most phenotypically pronounced diversification of the group has occurred in the Malagasy region, where 68 currently recognized species are divided among five genera. Here, we report the results of phylogenetic analyses of sequence data from the cytochrome c oxidase II and cytochrome b mitochondrial genes, for a total of 54 mycalesine taxa, mostly from Madagascar. These molecular data complement an existing data set based on male morphological characters. The molecular results support the suggestion from morphology that three of the five Malagasy genera are paraphyletic and support the monophyly of at least three major morphological clades. Novel hypotheses of terminal taxon pairs are generated by the molecular data. Dense taxon sampling appears to be crucial for elucidating phylogenetic relationships within this large radiation. A potentially complex scenario for the origin of Malagasy mycalesines is proposed.
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Affiliation(s)
- E Torres
- Department of Biology and Microbiology, California State University, Los Angeles, California 90032-8201, USA
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16
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Abstract
We used microsatellite DNA markers to genotype chicks in 10 broods of lek-breeding sage grouse, Centrocercus urophasianus, whose mothers' behaviour was studied by radio-tracking and observing leks. Previous behavioural studies suggested that almost all matings are performed by territorial males on leks and that multiple mating is rare. Two broods (20%) were sired by more than one male. Genetic analyses of the broods of eight females that visited an intensively studied lek were consistent with behavioural observations. Four females observed mating produced singly sired broods and males other than the individual observed copulating were excluded as sires for most or all of their chicks. Territorial males at the study lek were excluded as sires of broods of four other females that visited the lek but were not observed mating there. Radio-tracking suggested that two of these females mated at other leks. Our results confirm the reliability of mating observations at leks, but do not rule out a possible unseen component of the mating system.
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Affiliation(s)
- K Semple
- Department of Organismic Biology, Ecology and Evolution, University of California at Los Angeles, Los Angeles, CA 90095-1606, USA
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17
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Girman DJ, Vilà C, Geffen E, Creel S, Mills MG, McNutt JW, Ginsberg J, Kat PW, Mamiya KH, Wayne RK. Patterns of population subdivision, gene flow and genetic variability in the African wild dog (Lycaon pictus). Mol Ecol 2001; 10:1703-23. [PMID: 11472538 DOI: 10.1046/j.0962-1083.2001.01302.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
African wild dogs are large, highly mobile carnivores that are known to disperse over considerable distances and are rare throughout much of their geographical range. Consequently, genetic variation within and differentiation between geographically separated populations is predicted to be minimal. We determined the genetic diversity of mitochondrial DNA (mtDNA) control region sequences and microsatellite loci in seven populations of African wild dogs. Analysis of mtDNA nucleotide diversity suggests that, historically, wild dog populations have been small relative to other large carnivores. However, population declines due to recent habitat loss have not caused a dramatic reduction in genetic diversity. We found one historical and eight recent mtDNA genotypes in 280 individuals that defined two highly divergent clades. In contrast to a previous, more limited, mtDNA analysis, sequences from these clades are not geographically restricted to eastern or southern African populations. Rather, we found a large admixture zone spanning populations from Botswana, Zimbabwe and south-eastern Tanzania. Mitochondrial and microsatellite differentiation between populations was significant and unique mtDNA genotypes and alleles characterized the populations. However, gene flow estimates (Nm) based on microsatellite data were generally greater than one migrant per generation. In contrast, gene flow estimates based on the mtDNA control region were lower than expected given differences in the mode of inheritance of mitochondrial and nuclear markers which suggests a male bias in long-distance dispersal.
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Affiliation(s)
- D J Girman
- Department of Biology, Sonoma State University, Rohnert Park, CA, USA
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18
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Abstract
Domestication entails control of wild species and is generally regarded as a complex process confined to a restricted area and culture. Previous DNA sequence analyses of several domestic species have suggested only a limited number of origination events. We analyzed mitochondrial DNA (mtDNA) control region sequences of 191 domestic horses and found a high diversity of matrilines. Sequence analysis of equids from archaeological sites and late Pleistocene deposits showed that this diversity was not due to an accelerated mutation rate or an ancient domestication event. Consequently, high mtDNA sequence diversity of horses implies an unprecedented and widespread integration of matrilines and an extensive utilization and taming of wild horses. However, genetic variation at nuclear markers is partitioned among horse breeds and may reflect sex-biased dispersal and breeding.
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Affiliation(s)
- C Vilà
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, S-75236 Uppsala, Sweden.
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19
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Abstract
We examined cytochrome b sequence variation in 251 ornate shrews (Sorex ornatus) from 20 localities distributed throughout their geographical range. Additionally, vagrant (S. vagrans) and montane (S. monticolus) shrews from four localities were used as outgroups. We found 24 haplotypes in ornate shrews from California (USA) and Baja California (Mexico) that differed by 1-31 substitutions in 392 bp of mitochondrial DNA (mtDNA) sequence. In a subset of individuals, we sequenced 699 bp of cytochrome b to better resolve the phylogeographic relationships of populations. The ornate shrew is phylogeographically structured into three haplotype clades representing southern, central and northern localities. Analysis of allozyme variation reveals a similar pattern of variation. Several other small California vertebrates have a similar tripartite pattern of genetic subdivision. We suggest that topographic barriers and expansion and contraction of wetland habitats in the central valley during Pleistocene glacial cycles account for these patterns of genetic variation. Remarkably, the northern ornate shrew clade is phylogenetically clustered with another species of shrew suggesting that it may be a unique lowland form of the vagrant shrew that evolved in parallel to their southern California counterparts.
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Affiliation(s)
- J E Maldonado
- Department of Organismic Biology, Ecology and Evolution, University of California, Los Angeles 90095-1606, USA.
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20
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Abstract
In theory, genes under natural selection can be revealed by unique patterns of linkage disequilibrium (LD) and polymorphism at physically linked loci. However, given the effects of recombination and mutation, the physical extent and persistence of LD patterns in natural populations is uncertain. To assess the LD signature of selection, we survey variation in 26 microsatellite loci spanning an approximately 32-cM region that includes the warfarin-resistance gene (Rw) in five wild rat populations having resistance levels between 0 and 95%. We find a high frequency of heterozygote deficiency at microsatellite loci in resistant populations, and a negative association between gene diversity (H) and resistance. Contrary to previous studies, these data suggest that directional rather than overdominant selection may predominate during periods of intense anticoagulant treatment. In highly resistant populations, extensive LD was observed over a chromosome segment spanning approximately 14% of rat chromosome 1. In contrast, LD in a moderately resistant population was more localized and, in conjunction with likelihood ratios, allowed assignment of Rw to a 2. 2-cM interval. Within this genomic window, a diagnostic marker, D1Rat219, assigned 91% of rats to the correct resistance category. These results further demonstrate that "natural selection mapping" in field populations can detect and map major fitness-related genes, and question overdominance as the predominant mode of selection in anticoagulant-resistant rat populations.
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Affiliation(s)
- M H Kohn
- Department of Organismic Biology, Ecology, and Evolution (OBEE), University of California, Los Angeles, USA.
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21
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Abstract
Kinkajou social groups generally consist of one adult female, two males, one subadult and one juvenile. Based on analysis of variation in 11 microsatellite loci, we assess the degree of kinship within and between four social groups totaling 25 kinkajous. We use exclusion and likelihood analyses to assign parents for seven of the eight offspring sampled, five with >/= 95% certainty, and two with >/= 80% certainty. Five of six identified sires of group offspring came from the same social group as the mother and pup. Adult males and females within a group were unrelated and subadults and juveniles were offspring of the group adults, suggesting a family structure. All five identified paternities within a social group were by the dominant male of the group. However, this copulation asymmetry does not necessarily reflect cooperation due to kinship ties between the two adult males within a group as one of two adult male pairs sampled was unrelated. Neighbouring male kinkajous were more closely related to each other than neighbouring female kinkajous, suggesting that females disperse more often or farther than males.
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Affiliation(s)
- R W Kays
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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22
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Abstract
The Pleistocene was a dynamic period for Holarctic mammal species, complicated by episodes of glaciation, local extinctions, and intercontinental migration. The genetic consequences of these events are difficult to resolve from the study of present-day populations. To provide a direct view of population genetics in the late Pleistocene, we measured mitochondrial DNA sequence variation in seven permafrost-preserved brown bear (Ursus arctos) specimens, dated from 14,000 to 42,000 years ago. Approximately 36,000 years ago, the Beringian brown bear population had a higher genetic diversity than any extant North American population, but by 15,000 years ago genetic diversity appears similar to the modern day. The older, genetically diverse, Beringian population contained sequences from three clades now restricted to local regions within North America, indicating that current phylogeographic patterns may provide misleading data for evolutionary studies and conservation management. The late Pleistocene phylogeographic data also indicate possible colonization routes to areas south of the Cordilleran ice sheet.
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Affiliation(s)
- J A Leonard
- Department of Organismic Biology, University of California, Los Angeles, CA 90095-1606, USA
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23
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Vila C, Amorim IR, Leonard JA, Posada D, Castroviejo J, Petrucci-Fonseca F, Crandall KA, Ellegren H, Wayne RK. Mitochondrial DNA phylogeography and population history of the grey wolf canis lupus. Mol Ecol 1999; 8:2089-103. [PMID: 10632860 DOI: 10.1046/j.1365-294x.1999.00825.x] [Citation(s) in RCA: 274] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The grey wolf (Canis lupus) and coyote (C. latrans) are highly mobile carnivores that disperse over great distances in search of territories and mates. Previous genetic studies have shown little geographical structure in either species. However, population genetic structure is also influenced by past isolation events and population fluctuations during glacial periods. In this study, control region sequence data from a worldwide sample of grey wolves and a more limited sample of coyotes were analysed. The results suggest that fluctuating population sizes during the late Pleistocene have left a genetic signature on levels of variation in both species. Genealogical measures of nucleotide diversity suggest that historical population sizes were much larger in both species and grey wolves were more numerous than coyotes. Currently, about 300 000 wolves and 7 million coyotes exist. In grey wolves, genetic diversity is greater than that predicted from census population size, reflecting recent historical population declines. By contrast, nucleotide diversity in coyotes is smaller than that predicted by census population size, reflecting a recent population expansion following the extirpation of wolves from much of North America. Both species show little partitioning of haplotypes on continental or regional scales. However, a statistical parsimony analysis indicates local genetic structure that suggests recent restricted gene flow.
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24
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Abstract
The production of extreme or 'transgressive' phenotypes in segregating hybrid populations has been speculated to contribute to niche divergence of hybrid lineages. Here, we assess the frequency of transgressive segregation in hybrid populations, describe its genetic basis and discuss the factors that best predict its occurrence. From a survey of 171 studies that report phenotypic variation in segregating hybrid populations, we show that transgression is the rule rather than the exception. In fact, 155 of the 171 studies (91%) report at least one transgressive trait, and 44% of 1229 traits examined were transgressive. Transgression occurred most frequently in intraspecific crosses involving inbred, domesticated plant populations, and least frequently in interspecific crosses between outbred, wild animal species. Quantitative genetic studies of plant hybrids consistently point to the action of complementary genes as the primary cause of transgression, although overdominance and epistasis also contribute. Complementary genes appear to be common for most traits, with the possible exception of those with a history of disruptive selection. These results lend credence to the view that hybridization may provide the raw material for rapid adaptation and provide a simple explanation for niche divergence and phenotypic novelty often associated with hybrid lineages.
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Affiliation(s)
- L H Rieseberg
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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25
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Abstract
Population size is a fundamental biological parameter that is difficult to estimate. By genotyping coyote (Canis latrans) faeces systematically collected in the Santa Monica Mountains near Los Angeles, California, we exemplify a general, non-invasive method to census large mammals. Four steps are involved in the estimation. First, presumed coyote faeces are collected along paths or roadways where coyotes, like most carnivores, often defaecate and mark territorial boundaries. Second, DNA is extracted from the faeces and species identity and sex is determined by mitochondrial DNA and Y-chromosome typing. Third, hypervariable microsatellite loci are typed from the faeces. Lastly, rarefaction analysis is used to estimate population size from faecal genotypes. This method readily provides a point count estimate of population size and sex ratio. Additionally, we show that home range use paternity and kinship can be inferred from the distribution and relatedness patterns of faecal genotypes.
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Affiliation(s)
- M H Kohn
- Department of Biology, University of California, Los Angeles 90095-1606, USA.
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26
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Abstract
Comparative analysis of mammalian genomes provides important insight into the structure and function of genes. However, the comparative analysis of gene sequences from individuals of the same and different species also provides insight into the evolution of genes, populations, and species. We exemplify these two uses of genomic information. First, we document the evolutionary relationships of the domestic dog to other carnivores by using a variety of DNA-based information. A phylogenetic comparison of mitochondrial DNA sequences in dogs and gray wolves shows that dogs may have originated from multiple wolf populations at a time much earlier than suggested by the archaeologic record. We discuss previous theories about dog development and evolution in light of the new genetic data. Second, we review recent progress in dog genetic mapping due to the development of hypervariable markers and specific chromosome paints. Extensive genetic homology in gene order and function between humans and dogs has been discovered. The dog promises to be a valuable model for identifying genes that control morphologic differences between mammals as well as understanding genetically based disease.
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Affiliation(s)
- R K Wayne
- Department of Biology, University of California, Los Angeles 90095-1606, USA.
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Goldstein DB, Roemer GW, Smith DA, Reich DE, Bergman A, Wayne RK. The use of microsatellite variation to infer population structure and demographic history in a natural model system. Genetics 1999; 151:797-801. [PMID: 9927470 PMCID: PMC1460481 DOI: 10.1093/genetics/151.2.797] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.1] [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: 11/13/2022] Open
Abstract
To assess the reliability of genetic markers it is important to compare inferences that are based on them to a priori expectations. In this article we present an analysis of microsatellite variation within and among populations of island foxes (Urocyon littoralis) on California's Channel Islands. We first show that microsatellite variation at a moderate number of loci (19) can provide an essentially perfect description of the boundaries between populations and an accurate representation of their historical relationships. We also show that the pattern of variation across unlinked microsatellite loci can be used to test whether population size has been constant or increasing. Application of these approaches to the island fox system indicates that microsatellite variation may carry considerably more information about population history than is currently being used.
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Affiliation(s)
- D B Goldstein
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.
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28
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Abstract
The spectacular diversity in size, conformation, and pelage that characterizes the domestic dog reflects not only the intensity of artificial selection but ultimately the genetic variability of founding populations. Here we review past molecular genetic data that are relevant to understanding the origin and phylogenetic relationships of the dog. DNA-DNA hybridization data show that the dog family Canidae diverged about 50 million years ago from other carnivore families. In contrast, the extant canids are very closely related and diverged from a common ancestor about 10 million years ago. The evidence supporting a close relationship of dogs with gray wolves is overwhelming. However, dogs are remarkably diverse in mitochondrial and nuclear genes. Mitochondrial DNA analysis suggests a more ancient origin of dogs than has been indicated by the fossil record. In addition, dogs have originated from or interbred with wolves throughout their history at different times and different places. We test the possibility of an independent domestication event in North America by analysis of mtDNA variation in the Xoloitzcuintli. This unusual breed is believed to have been kept isolated for thousands of years and may be one of the most ancient breeds in North America. Our results do not support a New World domestication of dogs nor a close association of the Xoloitzcuintli with other hair-less breeds of dogs. Despite their phenotypic uniformity, the Xoloitzcuintli has a surprisingly high level of mtDNA sequence variation. Other breeds are also genetically diverse, suggesting that dog breeds were often founded with a large number of dogs from outbred populations.
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Affiliation(s)
- C Vilà
- Department of Biology, University of California, Los Angeles, USA.
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29
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Abstract
Genetic data suggest that red wolves (Canis rufus) resulted from a hybridization between coyotes (C. latrans) and grey wolves (C. lupus). The data of the hybridization, however, is uncertain. According to one hypothesis, the two species came into contact as coyotes increased their geographical range in conjunction with the advance of European settlers and as grey wolves were extirpated from the American south. Alternatively, the red wolves could have originated tens of thousands of years ago as a result of climate and habitat changes that disturbed the ecology of the two parent species. To obtain an upper limit on the date of hybridization that would help to distinguish the two scenarios, we compared microsatellite allele length distributions from red wolves, coyotes and grey wolves. Subject to the assumptions of our analysis, we conclude that the red wolves originated as a result of hybridizations that occurred during the past 12,800 years, and probably during the past 2500 years.
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Affiliation(s)
- D E Reich
- Department of Zoology, University of Oxford, UK
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31
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Abstract
We evaluate the relative effectiveness of four methods for preserving faecal samples for DNA analysis. PCR assays of fresh faecal samples collected from free-ranging baboons showed that amplification success was dependent on preservation method, PCR-product size, and whether nuclear or mitochondrial DNA was assayed. Storage in a DMSO/EDTA/Tris/salt solution (DETs) was most effective for preserving nuclear DNA, but storage in 70% ethanol, freezing at -20 degrees C and drying performed approximately equally well for mitochondrial DNA and short (< 200 bp) nuclear DNA fragments. Because faecal DNA is diluted and degraded, repeated extractions from faeces may be necessary and short nuclear markers should be employed for genotyping. A review of molecular scatology studies further suggests that three to six faeces per individual should be collected.
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Affiliation(s)
- M A Frantzen
- Department of Zoology and Entomology, University of Pretoria, South Africa.
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32
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Hadly EA, Kohn MH, Leonard JA, Wayne RK. A genetic record of population isolation in pocket gophers during Holocene climatic change. Proc Natl Acad Sci U S A 1998; 95:6893-6. [PMID: 9618509 PMCID: PMC22676 DOI: 10.1073/pnas.95.12.6893] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [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: 10/22/1997] [Accepted: 04/06/1998] [Indexed: 02/07/2023] Open
Abstract
A long-standing question in Quaternary paleontology is whether climate-induced, population-level phenotypic change is a result of large-scale migration or evolution in isolation. To directly measure genetic variation through time, ancient DNA and morphologic variation was measured over 2,400 years in a Holocene sequence of pocket gophers (Thomomys talpoides) from Lamar Cave, Yellowstone National Park, Wyoming. Ancient specimens and modern samples collected near Lamar Cave share mitochondrial cytochrome b sequences that are absent from adjacent localities, suggesting that the population was isolated for the entire period. In contrast, diastemal length, a morphologic character correlated with body size and nutritional level, changed predictably in response to climatic change. Our results demonstrate that small mammal populations can experience the long-term isolation assumed by many theoretical models of microevolutionary change.
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Affiliation(s)
- E A Hadly
- Mountain Research Center and Department of Biology, Montana State University, Bozeman, MT 59717, USA.
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33
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Abstract
A balance must be maintained between the proportion of individuals dispersing and the proportion remaining philopatric such that inbreeding and resource competition are minimized. Yet the relative importance of dispersal and philopatric behaviour is uncertain, especially for species with complex social systems. We examine the influence of dispersal on genetic relationships of a white-nosed coati (Nasua narica: Procyonidae) population from Panama. Field studies of the coati indicate a social system in which all females are highly philopatric and live in bands while all adult males become solitary at maturity, but do not disperse from the home range of their natal band. Based on analyses of multilocus DNA fingerprints, we confirm that female philopatry is the rule, long-distance dispersal is rare, and that relatedness between most bands is low. However, some new bands result from fission events and these bands retain relatively high relatedness to one another for several years. Adult males inhabiting the home range of a band are closely related to band members. In contrast, males and band members whose ranges do not overlap are unrelated or only slightly related. Adult males are also more closely related to other males whose home ranges they overlap extensively than to males whose home ranges they overlap only slightly. These results indicate that males initially disperse from their natal bands to reduce resource competition and not to avoid inbreeding. Inbreeding avoidance, if it occurs, results from more extensive range movements by males during the mating season.
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Affiliation(s)
- M E Gompper
- Department of Zoology, University of Tennessee, Knoxville 37996, USA.
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González S, Maldonado JE, Leonard JA, Vilà C, Duarte JM, Merino M, Brum-Zorrilla N, Wayne RK. Conservation genetics of the endangered Pampas deer (Ozotoceros bezoarticus). Mol Ecol 1998; 7:47-56. [PMID: 9465416 DOI: 10.1046/j.1365-294x.1998.00303.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [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: 02/06/2023]
Abstract
The Pampas deer (Ozotoceros bezoarticus L. 1758) is the most endangered neotropical cervid, and in the past occupied a wide range of open habitats including grassland, pampas, savanna, and cerrado (Brazil) from 5 degrees to 41 degrees S. To better understand the effect of habitat fragmentation on gene flow and genetic variation, and to uncover genetic units for conservation, we examined DNA sequences from the mitochondrial control region of 54 individuals from six localities distributed throughout the present geographical range of the Pampas deer. Our results suggest that the control region of the Pampas deer is one of the most polymorphic of any mammal. This remarkably high variability probably reflects large historic population sizes of millions of individuals in contrast to numbers of fewer than 80,000 today. Gene flow between populations is generally close to one migrant per generation and, with the exception of two populations from Argentina, all populations are significantly differentiated. The degree of gene flow was correlated with geographical distance between populations, a result consistent with limited dispersal being the primary determinant of genetic differentiation between populations. The molecular genetic results provide a mandate for habitat restoration and reintroduction of Pampas deer so that levels of genetic variation can be preserved and historic patterns of abundance can be reconstructed. However, the source of individuals for reintroduction generally should be from populations geographically closest to those now in danger of extinction.
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Affiliation(s)
- S González
- División Citogenética, IIBCE, Montevideo, Uruguay
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35
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Abstract
Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canidae fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canidae species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canidae endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canidae clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets.
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Affiliation(s)
- R K Wayne
- Department of Biology, University of California, Los Angeles, California 90095, USA
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36
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Faulkes CG, Abbott DH, O'Brien HP, Lau L, Roy MR, Wayne RK, Bruford MW. Micro- and macrogeographical genetic structure of colonies of naked mole-rats Heterocephalus glaber. Mol Ecol 1997; 6:615-28. [PMID: 9226945 DOI: 10.1046/j.1365-294x.1997.00227.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Patterns of genetic structure in eusocial naked mole-rat populations were quantified within and among geographically distant populations using multilocus DNA fingerprinting and mitochondrial DNA (mtDNA) sequence analysis. Individuals within colonies were genetically almost monomorphic, sharing the same mtDNA control region haplotype and having coefficients of band sharing estimated from DNA fingerprints ranging from 0.93 to 0.99. Family analysis of a hybrid captive colony of naked mole-rats with increased levels of genetic variability using multilocus DNA fingerprinting gave results consistent with Mendelian inheritance, and has revealed for the first time that multiple paternity can occur. In a survey of wild colonies from Ethiopia, Somalia and locations in northern and southern Kenya, we have examined mtDNA control region sequence variation in 42 individuals from 15 colonies, and together with multilocus DNA fingerprinting and mtDNA cytochrome-b sequence analysis in selected individuals have shown that these populations show considerable genetic divergence. Most of the variance in sequence divergence was found to be between geographical locations (phi ct = 0.68) and there was a significant correlation between sequence divergence and geographical separation of haplotypes. Six colonies from Mtito Andei in southern Kenya shared the same control region haplotype, suggesting a recent common maternal ancestor. In contrast, out of four colonies at Lerata in north Kenya, three haplotypes were identified, and phylogenetic analysis suggests that this area may be a zone where two distinct lineages are in close proximity. Genetic distances were maximal between Ethiopian and southern Kenyan populations at 5.8% for cytochrome-b, and are approaching interspecific values seen between other Bathyergids.
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Affiliation(s)
- C G Faulkes
- Conservation Genetics Group, Institute of Zoology, Zoological Society of London, UK.
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37
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Abstract
Mitochondrial DNA control region sequences were analyzed from 162 wolves at 27 localities worldwide and from 140 domestic dogs representing 67 breeds. Sequences from both dogs and wolves showed considerable diversity and supported the hypothesis that wolves were the ancestors of dogs. Most dog sequences belonged to a divergent monophyletic clade sharing no sequences with wolves. The sequence divergence within this clade suggested that dogs originated more than 100,000 years before the present. Associations of dog haplotypes with other wolf lineages indicated episodes of admixture between wolves and dogs. Repeated genetic exchange between dog and wolf populations may have been an important source of variation for artificial selection.
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Affiliation(s)
- C Vilà
- Department of Biology, University of California, Los Angeles, CA 90095-1606, USA
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38
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Altmann J, Alberts SC, Haines SA, Dubach J, Muruthi P, Coote T, Geffen E, Cheesman DJ, Mututua RS, Saiyalel SN, Wayne RK, Lacy RC, Bruford MW. Behavior predicts genes structure in a wild primate group. Proc Natl Acad Sci U S A 1996; 93:5797-801. [PMID: 8650172 PMCID: PMC39141 DOI: 10.1073/pnas.93.12.5797] [Citation(s) in RCA: 259] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The predictability of genetic structure from social structure and differential mating success was tested in wild baboons. Baboon populations are subdivided into cohesive social groups that include multiple adults of both sexes. As in many mammals, males are the dispersing sex. Social structure and behavior successfully predicted molecular genetic measures of relatedness and variance in reproductive success. In the first quantitative test of the priority-of-access model among wild primates, the reproductive priority of dominant males was confirmed by molecular genetic analysis. However, the resultant high short-term variance in reproductive success did not translate into equally high long-term variance because male dominance status was unstable. An important consequence of high but unstable short-term variance is that age cohorts will tend to be paternal sibships and social groups will be genetically substructured by age.
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Affiliation(s)
- J Altmann
- Department of Ecology and Evolution, University of Chicago, IL 60637, USA
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40
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Stanley HF, Casey S, Carnahan JM, Goodman S, Harwood J, Wayne RK. Worldwide patterns of mitochondrial DNA differentiation in the harbor seal (Phoca vitulina). Mol Biol Evol 1996; 13:368-82. [PMID: 8587502 DOI: 10.1093/oxfordjournals.molbev.a025596] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.3] [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: 01/31/2023] Open
Abstract
The harbor seal (Phoca vitulina) has one of the broadest geographic distributions of any pinniped, stretching from the east Baltic, west across the Atlantic and Pacific Oceans to southern Japan. Although individuals may travel several hundred kilometers on annual feeding migrations, harbor seals are generally believed to be philopatric, returning to the same areas each year to breed. Consequently, seals from different areas are likely to be genetically differentiated, with levels of genetic divergence increasing with distance. Differentiation may also be caused by long-standing topographic barriers such as the polar sea ice. We analyzed samples of 227 harbor seals from 24 localities and defined 34 genotypes based on 435 bp of control region sequence. Phylogenetic analysis and analysis of molecular variance showed that populations in the Atlantic and Pacific Oceans and east and west coast populations of these oceans are significantly differentiated. Within these four regions, populations that are geographically farthest apart generally are the most differentiated and often do not share genotypes or differ in genotype frequency. The average corrected sequence divergence between populations in the Atlantic and Pacific Oceans is 3.28% +/- 0.38% and those among populations within each of these oceans are 0.75% +/- 0.69% and 1.19% +/- 0.65%, respectively. Our results suggest that harbor seals are regionally philopatric, on the scale of several hundred kilometers. However, genetic discontinuities may exist, even between neighboring populations such as those on the Scottish and east English coasts or the east and west Baltic. The mitochondrial data are consistent with an ancient isolation of populations in both oceans, due to the development of polar sea ice. In the Atlantic and Pacific, populations appear to have been colonized from west to east with the European populations showing the most recent common ancestry. We suggest the recent ancestry of European seal populations may reflect recolonization from Ice Age refugia after the last glaciation.
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Affiliation(s)
- H F Stanley
- Institute of Zoology, Zoological Society of London, UK
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41
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Affiliation(s)
- R K Wayne
- University of California, Los Angeles, USA
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42
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Abstract
Serum samples from 76 free-ranging adult jackals of three species from four localities in Kenya were examined for circulating antibodies against four canine pathogens: rabies virus, canine parvovirus (CPV-2), canine distemper virus (CDV), and Ehrlichia canis. Samples were collected between April 1987 and January 1988. Among black-backed jackals (Canis mesomelas), the most sampled species, the mean prevalence of antibodies to CPV-2, CDV, rabies virus, and E. canis was 34% (14 positive/55 sampled), 9% (4/55), 3% (1/28), and 2% (1/36), respectively. There were no significantly differences among sampling locations. In one area, antibody prevalence of CPV-2 was significantly higher for golden jackals (C. aureus; 9/16) than for C. mesomelas (5/26). Only three side-striped jackals (C. adustus) were sampled, but antibodies to CPV-2 and CDV were present. As jackals often are the most abundant wild carnivore in African ecosystems, they could serve as an important indicator species to monitor the potential of exposure of rare and endangered canids to specific canine diseases.
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Affiliation(s)
- K A Alexander
- Department of Veterinary Pathology, Microbiology, and Immunology, University of California, Davis 95616
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Gottelli D, Sillero-Zubiri C, Applebaum GD, Roy MS, Girman DJ, Garcia-Moreno J, Ostrander EA, Wayne RK. Molecular genetics of the most endangered canid: the Ethiopian wolf Canis simensis. Mol Ecol 1994; 3:301-12. [PMID: 7921357 DOI: 10.1111/j.1365-294x.1994.tb00070.x] [Citation(s) in RCA: 243] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The world's most endangered canid is the Ethiopian wolf Canis simensis, which is found in six isolated areas of the Ethiopian highlands with a total population of no more than 500 individuals. Ethiopian wolf populations are declining due to habitat loss and extermination by humans. Moreover, in at least one population, Ethiopian wolves are sympatric with domestic dogs, which may hybridize with them, compete for food, and act as disease vectors. Using molecular techniques, we address four questions concerning Ethiopian wolves that have conservation implications. First, we determine the relationships of Ethiopian wolves to other wolf-like canids by phylogenetic analysis of 2001 base pairs of mitochondrial DNA (mtDNA) sequence. Our results suggest that the Ethiopian wolf is a distinct species more closely related to gray wolves and coyotes than to any African canid. The mtDNA sequence similarity with gray wolves implies that the Ethiopian wolf may hybridize with domestic dogs, a recent derivative of the gray wolf. We examine this possibility through mtDNA restriction fragment analysis and analysis of nine microsatellite loci in populations of Ethiopian wolves. The results imply that hybridization has occurred between female Ethiopian wolves and male domestic dogs in one population. Finally, we assess levels of variability within and between two Ethiopian wolf populations. Although these closely situated populations are not differentiated, the level of variability in both is low, suggesting long-term effective population sizes of less than a few hundred individuals. We recommend immediate captive breeding of Ethiopian wolves to protect their gene pool from dilution and further loss of genetic variability.
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Affiliation(s)
- D Gottelli
- Institute of Zoology, Zoological Society of London, UK
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44
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Abstract
We investigate the utility of hypervariable microsatellite loci to measure genetic variability remaining in the northern hairy-nosed wombat, one of Australia's rarest mammals. This species suffered a dramatic range and population reduction over the past 120 years and now exists as a single colony of about 70 individuals at Epping Forest National Park, central Queensland. Because our preliminary research on mitochondrial DNA and multilocus DNA fingerprints did not reveal informative variation in this population, we chose to examine variation in microsatellite repeats, a class of loci known to be highly polymorphic in mammals. To assess the suitability of various wombat populations as a reference for comparisons of genetic variability and subdivision we further analysed mitochondrial DNA cytochrome b sequence, using phylogenetic methods. Our results show that appreciable levels of variation still exist in the Epping Forest colony although it has only 41% of the heterozygosity shown in a population of a closely-related species. From museum specimens collected in 1884, we also assessed microsatellite variation in an extinct population of the northern hairy-nosed wombat, from Deniliquin, New South Wales, 2000 km to the south of the extant population. The apparent loss of variation in the Epping Forest colony is consistent with an extremely small effective population size throughout its 120-year decline.
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Affiliation(s)
- A C Taylor
- Institute of Zoology, Zoological Society of London, UK
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45
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Roy MS, Geffen E, Smith D, Ostrander EA, Wayne RK. Patterns of differentiation and hybridization in North American wolflike canids, revealed by analysis of microsatellite loci. Mol Biol Evol 1994; 11:553-70. [PMID: 8078397 DOI: 10.1093/oxfordjournals.molbev.a040137] [Citation(s) in RCA: 31] [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] [Indexed: 01/28/2023] Open
Abstract
Genetic divergence and gene flow among closely related populations are difficult to measure because mutation rates of most nuclear loci are so low that new mutations have not had sufficient time to appear and become fixed. Microsatellite loci are repeat arrays of simple sequences that have high mutation rates and are abundant in the eukaryotic genome. Large population samples can be screened for variation by using the polymerase chain reaction and polyacrylamide gel electrophoresis to separate alleles. We analyzed 10 microsatellite loci to quantify genetic differentiation and hybridization in three species of North American wolflike canids. We expected to find a pattern of genetic differentiation by distance to exist among wolflike canid populations, because of the finite dispersal distances of individuals. Moreover, we predicted that, because wolflike canids are highly mobile, hybrid zones may be more extensive and show substantial changes in allele frequency, relative to nonhybridizing populations. We demonstrate that wolves and coyotes do not show a pattern of genetic differentiation by distance. Genetic subdivision in coyotes, as measured by theta and Gst, is not significantly different from zero, reflecting persistent gene flow among newly established populations. However, gray wolves show significant subdivision that may be either due to drift in past Ice Age refugia populations or a result of other causes. Finally, in areas where gray wolves and coyotes hybridize, allele frequencies of gray wolves are affected, but those of coyotes are not. Past hybridization between the two species in the south-central United States may account for the origin of the red wolf.
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Affiliation(s)
- M S Roy
- Institute of Zoology, Zoological Society of London, United Kingdom
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46
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Roy MS, Girman DJ, Taylor AC, Wayne RK. The use of museum specimens to reconstruct the genetic variability and relationships of extinct populations. Experientia 1994; 50:551-7. [PMID: 8020615 DOI: 10.1007/bf01921724] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In this review, we discuss the use of DNA from museum specimens to address conservation genetic questions. We provide four examples from our previous studies of the northern hairy-nosed wombat, African wild dog, Ethiopian wolf and red wolf. These species were genetically surveyed using two molecular approaches: first, analysis of short sequences in the mitochondrial genome using species-specific primers, and second, analysis of hypervariable microsatellite loci. The studies demonstrate that museum-derived DNA adds an important dimension to the genetic study of extant populations. Inaccessible populations can be studied, and both the loss of genetic variation and its distribution over space and time can be better understood. Finally, analysis of additional museum material provides definitive evidence for a hybrid origin of the red wolf.
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Affiliation(s)
- M S Roy
- Institute of Zoology, Zoological Society of London, England, UK
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47
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Abstract
Microsatellites may soon become the markers of choice for molecular population genetic studies. However, our knowledge of these simple repetitive sequences and how they evolve in natural populations is far from complete. We highlight some recent results of population studies and advances in our ability to interpret some of the allele frequency distributions that we are beginning to observe.
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Affiliation(s)
- M W Bruford
- Conservation Genetics Group, Institute of Zoology, Regent's Park, London, UK
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48
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49
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Girman DJ, Kat PW, Mills MG, Ginsberg JR, Borner M, Wilson V, Fanshawe JH, Fitzgibbon C, Lau LM, Wayne RK. Molecular genetic and morphological analyses of the African wild dog (Lycaon pictus). J Hered 1993; 84:450-9. [PMID: 7903676 DOI: 10.1093/oxfordjournals.jhered.a111371] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
African wild dog populations have declined precipitously during the last 100 years in eastern Africa. The possible causes of this decline include a reduction in prey abundance and habitat; disease; and loss of genetic variability accompanied by inbreeding depression. We examined the levels of genetic variability and distinctiveness among populations of African wild dogs using mitochondrial DNA (mtDNA) restriction site and sequence analyses and multivariate analysis of cranial and dental measurements. Our results indicate that the genetic variability of eastern African wild dog populations is comparable to that of southern Africa and similar to levels of variability found in other large canids. Southern and eastern populations of wild dogs show about 1% divergence in mtDNA sequence and form two monophyletic assemblages containing three mtDNA genotypes each. No genotypes are shared between the two regions. With one exception, all wild dogs examined from zoos had southern African genotypes. Morphological analysis supports the distinction of eastern and southern African wild dog populations, and we suggest they should be considered separate subspecies. An eastern African wild dog breeding program should be initiated to ensure preservation of the eastern African form and to slow the loss of genetic variability that, while not yet apparent, will inevitably occur if wild populations continue to decline. Finally, we examined the phylogenetic relationships of wild dogs to other wolf-like canids through analysis of 736 base pairs (bp) of cytochrome b sequence and showed wild dogs to belong to a phylogenetically distinct lineage of the wolf-like canids.
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Affiliation(s)
- D J Girman
- Department of Biology, University of California, Los Angeles 90024
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Abstract
Molecular genetic tools have been used to dissect the evolutionary relationships of the dog-like carnivores, revealing their place in the order Carnivora, the relationships of species within the family Canidae, and the genetic exchange that occurs among conspecific populations. High rates of gene flow among populations within some species, such as the coyote and gray wolf, have suppressed genetic divergence, and where these species hybridize, large hybrid zones have been formed. In fact, the phenotype of the endangered American red wolf may be strongly influenced by hybridization with coyotes and gray wolves. Hybridization and habitat fragmentation greatly complicate plans to conserve the genetic diversity of wild canids.
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Affiliation(s)
- R K Wayne
- Institute of Zoology, Zoological Society of London, UK
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