3
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Warmuth VM, Burgess MD, Laaksonen T, Manica A, Mägi M, Nord A, Primmer CR, Sætre GP, Winkel W, Ellegren H. Major population splits coincide with episodes of rapid climate change in a forest-dependent bird. Proc Biol Sci 2021; 288:20211066. [PMID: 34727712 PMCID: PMC8564624 DOI: 10.1098/rspb.2021.1066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/07/2021] [Indexed: 11/17/2022] Open
Abstract
Climate change influences population demography by altering patterns of gene flow and reproductive isolation. Direct mutation rates offer the possibility for accurate dating on the within-species level but are currently only available for a handful of vertebrate species. Here, we use the first directly estimated mutation rate in birds to study the evolutionary history of pied flycatchers (Ficedula hypoleuca). Using a combination of demographic inference and species distribution modelling, we show that all major population splits in this forest-dependent system occurred during periods of increased climate instability and rapid global temperature change. We show that the divergent Spanish subspecies originated during the Eemian-Weichselian transition 115-104 thousand years ago (kya), and not during the last glacial maximum (26.5-19 kya), as previously suggested. The magnitude and rates of climate change during the glacial-interglacial transitions that preceded population splits in pied flycatchers were similar to, or exceeded, those predicted to occur in the course of the current, human-induced climate crisis. As such, our results provide a timely reminder of the strong impact that episodes of climate instability and rapid temperature changes can have on species' evolutionary trajectories, with important implications for the natural world in the Anthropocene.
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Affiliation(s)
- Vera M. Warmuth
- Department of Evolutionary Biology, Biozentrum Martinsried, Ludwig-Maximilians Universität München, Planegg-Martinsried, Germany
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Malcolm D. Burgess
- Centre for Animal Behaviour, University of Exeter, Exeter, UK
- RSPB Centre for Conservation Science, Sandy, UK
| | - Toni Laaksonen
- Department of Biology, University of Turku, Turku, Finland
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Marko Mägi
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Andreas Nord
- Department of Biology, Section for Evolutionary Ecology, Lund University, Lund, Sweden
| | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Program, University of Helsinki, Finland
- Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Finland
| | - Glenn-Peter Sætre
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Wolfgang Winkel
- Institute of Avian Research, ‘Vogelwarte Helgoland’, Wilhelmshaven, Germany
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
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4
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Weissensteiner MH, Bunikis I, Catalán A, Francoijs KJ, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Author Correction: Discovery and population genomics of structural variation in a songbird genus. Nat Commun 2021; 12:3163. [PMID: 34017009 PMCID: PMC8138003 DOI: 10.1038/s41467-021-23640-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden. .,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany. .,Department of Biology, Pennsylvania State University, 310 Wartik Lab, PA, 16802, USA.
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815752 37, Uppsala, Sweden
| | - Ana Catalán
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | | | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Wieland Heim
- Institute of Landscsape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
| | - Valentina Peona
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.,Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Saurabh D Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.,Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Alexander Suh
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.,Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Vera M Warmuth
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden. .,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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5
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Gemmell NJ, Rutherford K, Prost S, Tollis M, Winter D, Macey JR, Adelson DL, Suh A, Bertozzi T, Grau JH, Organ C, Gardner PP, Muffato M, Patricio M, Billis K, Martin FJ, Flicek P, Petersen B, Kang L, Michalak P, Buckley TR, Wilson M, Cheng Y, Miller H, Schott RK, Jordan MD, Newcomb RD, Arroyo JI, Valenzuela N, Hore TA, Renart J, Peona V, Peart CR, Warmuth VM, Zeng L, Kortschak RD, Raison JM, Zapata VV, Wu Z, Santesmasses D, Mariotti M, Guigó R, Rupp SM, Twort VG, Dussex N, Taylor H, Abe H, Bond DM, Paterson JM, Mulcahy DG, Gonzalez VL, Barbieri CG, DeMeo DP, Pabinger S, Van Stijn T, Clarke S, Ryder O, Edwards SV, Salzberg SL, Anderson L, Nelson N, Stone C. The tuatara genome reveals ancient features of amniote evolution. Nature 2020; 584:403-409. [PMID: 32760000 PMCID: PMC7116210 DOI: 10.1038/s41586-020-2561-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/26/2020] [Indexed: 12/21/2022]
Abstract
The tuatara (Sphenodon punctatus)-the only living member of the reptilian order Rhynchocephalia (Sphenodontia), once widespread across Gondwana1,2-is an iconic species that is endemic to New Zealand2,3. A key link to the now-extinct stem reptiles (from which dinosaurs, modern reptiles, birds and mammals evolved), the tuatara provides key insights into the ancestral amniotes2,4. Here we analyse the genome of the tuatara, which-at approximately 5 Gb-is among the largest of the vertebrate genomes yet assembled. Our analyses of this genome, along with comparisons with other vertebrate genomes, reinforce the uniqueness of the tuatara. Phylogenetic analyses indicate that the tuatara lineage diverged from that of snakes and lizards around 250 million years ago. This lineage also shows moderate rates of molecular evolution, with instances of punctuated evolution. Our genome sequence analysis identifies expansions of proteins, non-protein-coding RNA families and repeat elements, the latter of which show an amalgam of reptilian and mammalian features. The sequencing of the tuatara genome provides a valuable resource for deep comparative analyses of tetrapods, as well as for tuatara biology and conservation. Our study also provides important insights into both the technical challenges and the cultural obligations that are associated with genome sequencing.
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Affiliation(s)
- Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand.
| | - Kim Rutherford
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Marc Tollis
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, USA
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - David L Adelson
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Terry Bertozzi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - José H Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen, Berlin, Germany
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chris Organ
- Department of Earth Sciences, Montana State University, Bozeman, MT, USA
| | - Paul P Gardner
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bent Petersen
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lin Kang
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
| | - Pawel Michalak
- Edward Via College of Osteopathic Medicine, Blacksburg, VA, USA
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Thomas R Buckley
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Melissa Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Yuanyuan Cheng
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | | | - Ryan K Schott
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Melissa D Jordan
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - Richard D Newcomb
- The New Zealand Institute for Plant and Food Research, Auckland, New Zealand
| | - José Ignacio Arroyo
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Tim A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Jaime Renart
- Instituto de Investigaciones Biomédicas 'Alberto Sols' CSIC-UAM, Madrid, Spain
| | - Valentina Peona
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
| | - Claire R Peart
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Vera M Warmuth
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilian University of Munich, Planegg-Martinsried, Germany
| | - Lu Zeng
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Joy M Raison
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shawn M Rupp
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Victoria G Twort
- Manaaki Whenua - Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nicolas Dussex
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Helen Taylor
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Hideaki Abe
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Donna M Bond
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - James M Paterson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Vanessa L Gonzalez
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | | | - Stephan Pabinger
- Austrian Institute of Technology (AIT), Center for Health and Bioresources, Molecular Diagnostics, Vienna, Austria
| | | | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Oliver Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology and the Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay Anderson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nicola Nelson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Clive Stone
- Ngatiwai Trust Board, Whangarei, New Zealand
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6
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Weissensteiner MH, Bunikis I, Catalán A, Francoijs KJ, Knief U, Heim W, Peona V, Pophaly SD, Sedlazeck FJ, Suh A, Warmuth VM, Wolf JBW. Discovery and population genomics of structural variation in a songbird genus. Nat Commun 2020; 11:3403. [PMID: 32636372 PMCID: PMC7341801 DOI: 10.1038/s41467-020-17195-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/16/2020] [Indexed: 02/07/2023] Open
Abstract
Structural variation (SV) constitutes an important type of genetic mutations providing the raw material for evolution. Here, we uncover the genome-wide spectrum of intra- and interspecific SV segregating in natural populations of seven songbird species in the genus Corvus. Combining short-read (N = 127) and long-read re-sequencing (N = 31), as well as optical mapping (N = 16), we apply both assembly- and read mapping approaches to detect SV and characterize a total of 220,452 insertions, deletions and inversions. We exploit sampling across wide phylogenetic timescales to validate SV genotypes and assess the contribution of SV to evolutionary processes in an avian model of incipient speciation. We reveal an evolutionary young (~530,000 years) cis-acting 2.25-kb LTR retrotransposon insertion reducing expression of the NDP gene with consequences for premating isolation. Our results attest to the wealth and evolutionary significance of SV segregating in natural populations and highlight the need for reliable SV genotyping.
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Affiliation(s)
- Matthias H Weissensteiner
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
- Department of Biology, Pennsylvania State University, 310 Wartik Lab, University Park, PA, 16802, USA.
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, 752 37, Uppsala, Sweden
| | - Ana Catalán
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | | | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Wieland Heim
- Institute of Landscsape Ecology, University of Münster, Heisenbergstrasse 2, 48149, Münster, Germany
| | - Valentina Peona
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
| | - Saurabh D Pophaly
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center at Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Alexander Suh
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden
- Department of Organismal Biology - Systematic Biology, Uppsala University, 752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Vera M Warmuth
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Evolutionary Biology and Science for Life Laboratory, Uppsala University, 752 36, Uppsala, Sweden.
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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