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Skirgård H, Haynie HJ, Blasi DE, Hammarström H, Collins J, Latarche JJ, Lesage J, Weber T, Witzlack-Makarevich A, Passmore S, Chira A, Maurits L, Dinnage R, Dunn M, Reesink G, Singer R, Bowern C, Epps P, Hill J, Vesakoski O, Robbeets M, Abbas NK, Auer D, Bakker NA, Barbos G, Borges RD, Danielsen S, Dorenbusch L, Dorn E, Elliott J, Falcone G, Fischer J, Ghanggo Ate Y, Gibson H, Göbel HP, Goodall JA, Gruner V, Harvey A, Hayes R, Heer L, Herrera Miranda RE, Hübler N, Huntington-Rainey B, Ivani JK, Johns M, Just E, Kashima E, Kipf C, Klingenberg JV, König N, Koti A, Kowalik RG, Krasnoukhova O, Lindvall NL, Lorenzen M, Lutzenberger H, Martins TR, Mata German C, van der Meer S, Montoya Samamé J, Müller M, Muradoglu S, Neely K, Nickel J, Norvik M, Oluoch CA, Peacock J, Pearey IO, Peck N, Petit S, Pieper S, Poblete M, Prestipino D, Raabe L, Raja A, Reimringer J, Rey SC, Rizaew J, Ruppert E, Salmon KK, Sammet J, Schembri R, Schlabbach L, Schmidt FW, Skilton A, Smith WD, de Sousa H, Sverredal K, Valle D, Vera J, Voß J, Witte T, Wu H, Yam S, Ye J, Yong M, Yuditha T, Zariquiey R, Forkel R, Evans N, Levinson SC, Haspelmath M, Greenhill SJ, Atkinson QD, Gray RD. Grambank reveals the importance of genealogical constraints on linguistic diversity and highlights the impact of language loss. Sci Adv 2023; 9:eadg6175. [PMID: 37075104 PMCID: PMC10115409 DOI: 10.1126/sciadv.adg6175] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
While global patterns of human genetic diversity are increasingly well characterized, the diversity of human languages remains less systematically described. Here, we outline the Grambank database. With over 400,000 data points and 2400 languages, Grambank is the largest comparative grammatical database available. The comprehensiveness of Grambank allows us to quantify the relative effects of genealogical inheritance and geographic proximity on the structural diversity of the world's languages, evaluate constraints on linguistic diversity, and identify the world's most unusual languages. An analysis of the consequences of language loss reveals that the reduction in diversity will be strikingly uneven across the major linguistic regions of the world. Without sustained efforts to document and revitalize endangered languages, our linguistic window into human history, cognition, and culture will be seriously fragmented.
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Affiliation(s)
- Hedvig Skirgård
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- Department of Linguistics, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Corresponding author. (H.S.); (R.D.G.)
| | - Hannah J. Haynie
- Department of Linguistics, University of Colorado Boulder, Boulder, CO, USA
| | - Damián E. Blasi
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Human Relation Area Files, Yale University, New Haven, CT, USA
| | - Harald Hammarström
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Department of Linguistics and Philology, Uppsala University, Uppsala, Sweden
| | - Jeremy Collins
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Department of Linguistics, Faculty of Arts, Radboud University, Nijmegen, Netherlands
| | - Jay J. Latarche
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Jakob Lesage
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Langage, Langues et Cultures d'Afrique (LLACAN), Centre National de la Recherche Scientifique (CNRS), Villejuif, France
- Institut National des Langues et Civilisations Orientales (INALCO), Paris, France
- Department of Asian and African Studies, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tobias Weber
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Alena Witzlack-Makarevich
- Department of Linguistics, Faculty of Humanities, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sam Passmore
- Evolution of Cultural Diversity Initiative, School of Culture, History and Language, College of Asia and the Pacific, The Australian National University, Canberra, ACT, Australia
- Faculty of Environment and Information Studies, Keio University SFC (Shonan Fujisawa Campus), Tokyo, Japan
- Department of Anthropology and Archaeology, Faculty of Arts, University of Bristol, Bristol, UK
| | - Angela Chira
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Luke Maurits
- Department of Comparative Cultural Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Russell Dinnage
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, FL, USA
| | - Michael Dunn
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Department of Linguistics and Philology, Uppsala University, Uppsala, Sweden
| | - Ger Reesink
- Department of Linguistics, Faculty of Arts, Radboud University, Nijmegen, Netherlands
| | - Ruth Singer
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- Research Unit for Indigenous Language, School of Languages and Linguistics, University of Melbourne, Melbourne, Australia
| | - Claire Bowern
- Department of Linguistics, Yale University, New Haven, CT, USA
| | - Patience Epps
- Department of Linguistics, University of Texas at Austin, Austin, TX, USA
| | - Jane Hill
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Outi Vesakoski
- Department of Biology, Turku University, Turku, Finland
- Department of Finnish and Finno-Ugric languages, University of Turku, Turku, Finland
| | - Martine Robbeets
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Noor Karolin Abbas
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Daniel Auer
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nancy A. Bakker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Giulia Barbos
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Robert D. Borges
- Institute of Slavic Studies, Polish Academy of Sciences, Warsaw, Poland
| | - Swintha Danielsen
- Zentrum für Kleine und Regionale Sprachen, Friesisches Seminar, Europa-Universität Flensburg, Flensburg, Germany
- Centro de Investigaciones Históricas y Antropológicas (CIHA), Santa Cruz de la Sierra, Bolivia
- Europa-Universität Flensburg (EUF), Flensburg, Germany
| | - Luise Dorenbusch
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Linguistics, Leipzig University, Leipzig, Germany
| | - Ella Dorn
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - John Elliott
- Department of Linguistics, University of Hawaiʻi at Mānoa, Honolulu, HI, USA
| | - Giada Falcone
- Department of Linguistics and Philology, Uppsala University, Uppsala, Sweden
| | - Jana Fischer
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Yustinus Ghanggo Ate
- Department of Linguistics, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- Universitas Katolik Weetebula, Sumba Island, Indonesia
| | - Hannah Gibson
- Department of Languages and Linguistics, University of Essex, Essex, UK
| | - Hans-Philipp Göbel
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Department of Linguistics, University of Cologne, Cologne, Germany
| | - Jemima A. Goodall
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Victoria Gruner
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Andrew Harvey
- Faculty of Languages and Literatures, University of Bayreuth, Bayreuth, Germany
| | - Rebekah Hayes
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Leonard Heer
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Roberto E. Herrera Miranda
- Institut National des Langues et Civilisations Orientales (INALCO), Paris, France
- Institute of Linguistics, Leipzig University, Leipzig, Germany
- Structure et Dynamique des Langues (SeDyl), Centre National de la Recherche Scientifique (CNRS), Villejuif, France
- Sprachwissenschaftliches Seminar, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Nataliia Hübler
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Biu Huntington-Rainey
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
- Division of Psychology and Language Sciences, Faculty of Brain Sciences, University College London (UCL), University of London, London, UK
- Institutt for Filosofi, ide- og Kunsthistorie og Klassiske Språk (IFIKK), Det Humanistisk Fakultet, Universitet i Oslo, Oslo, Norway
| | - Jessica K. Ivani
- Department of Comparative Linguistics, University of Zürich, Zürich, Switzerland
| | - Marilen Johns
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Erika Just
- Department of Comparative Linguistics, University of Zürich, Zürich, Switzerland
| | - Eri Kashima
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- Department of Linguistics, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
| | - Carolina Kipf
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Janina V. Klingenberg
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Nikita König
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Department of Linguistics, European University Viadrina, Frankfur an der Oder, Germany
| | - Aikaterina Koti
- Department of Linguistics and Philology, Uppsala University, Uppsala, Sweden
| | | | - Olga Krasnoukhova
- Centre for Linguistics, Leiden University, Leiden, Netherlands
- Department of Linguistics, University of Antwerpen, Antwerpen, Belgium
| | - Nora L. M. Lindvall
- Department of Linguistics and Philology, Uppsala University, Uppsala, Sweden
| | - Mandy Lorenzen
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hannah Lutzenberger
- Department of Linguistics, Faculty of Arts, Radboud University, Nijmegen, Netherlands
- Department of English Language and Linguistics, University of Birmingham, Birmingham, UK
| | - Tânia R. A. Martins
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Celia Mata German
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Suzanne van der Meer
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Jaime Montoya Samamé
- Facultad de Letras y Ciencias Humanas, Pontificia Universidad Católica del Perú, Lima, Perú
| | - Michael Müller
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Saliha Muradoglu
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
| | - Kelsey Neely
- Department of Linguistics, University of Texas at Austin, Austin, TX, USA
| | - Johanna Nickel
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Miina Norvik
- Institute of Estonian and General Linguistics, University of Tartu, Tartu, Estonia
- Department of Modern Languages, Uppsala University, Uppsala, Sweden
| | - Cheryl Akinyi Oluoch
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Jesse Peacock
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Department of Linguistics, Faculty of Arts, Radboud University, Nijmegen, Netherlands
| | - India O. C. Pearey
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Naomi Peck
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- University of Freiburg, Freiburg, Germany
| | - Stephanie Petit
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Sören Pieper
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Mariana Poblete
- Facultad de Letras y Ciencias Humanas, Pontificia Universidad Católica del Perú, Lima, Perú
- Universidad de Chile, Santiago, Chile
| | - Daniel Prestipino
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
| | - Linda Raabe
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Amna Raja
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Janis Reimringer
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sydney C. Rey
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
- The Language Conservancy, Bloomington, IN, USA
| | - Julia Rizaew
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Eloisa Ruppert
- Department of Linguistics, Quantitative Lexicology and Variational Linguistics (QLVL), KU Leuven, Leuven, Belgium
| | - Kim K. Salmon
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jill Sammet
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Rhiannon Schembri
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Lars Schlabbach
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | | | - Amalia Skilton
- Department of Linguistics, Cornell University, Ithaca, NY, USA
| | | | - Hilário de Sousa
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
- Centre de Recherches Linguistiques sur l'Asie Orientale (CRLAO), École des Hautes Études en Sciences Sociales (EHESS), Aubervilliers, France
| | - Kristin Sverredal
- Department of Linguistics and Philology, Uppsala University, Uppsala, Sweden
| | - Daniel Valle
- Department of Modern Languages, University of Mississippi, Oxford, MS, USA
| | - Javier Vera
- Facultad de Letras y Ciencias Humanas, Pontificia Universidad Católica del Perú, Lima, Perú
| | - Judith Voß
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Tim Witte
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Frisian and General Linguistics, Department of General Linguistics, Institute for Scandinavian Studies, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Henry Wu
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- International College for Postgraduate Buddhist Studies, Tokyo, Japan
| | - Stephanie Yam
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- Institute for General Linguistics, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jingting Ye
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chinese Language and Literature, Fudan University, Shanghai, China
| | - Maisie Yong
- Department of Linguistics, School of Languages, Cultures and Linguistics, School of Oriental and African Studies (SOAS), University of London, London, UK
| | - Tessa Yuditha
- Department of Linguistics, Faculty of Arts, Radboud University, Nijmegen, Netherlands
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Seville, Spain
| | - Roberto Zariquiey
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Facultad de Letras y Ciencias Humanas, Pontificia Universidad Católica del Perú, Lima, Perú
| | - Robert Forkel
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nicholas Evans
- ARC Centre of Excellence for the Dynamics of Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
- Department of Linguistics, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australia
| | - Stephen C. Levinson
- Department of Language and Cognition, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Martin Haspelmath
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Simon J. Greenhill
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Psychology, University of Auckland, Auckland, New Zealand
| | | | - Russell D. Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Psychology, University of Auckland, Auckland, New Zealand
- Corresponding author. (H.S.); (R.D.G.)
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5
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Eichinger L, Pachebat J, Glöckner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Babu MM, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail M, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox E, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A. The genome of the social amoeba Dictyostelium discoideum. Nature 2005; 435:43-57. [PMID: 15875012 PMCID: PMC1352341 DOI: 10.1038/nature03481] [Citation(s) in RCA: 947] [Impact Index Per Article: 49.8] [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] [Received: 09/16/2004] [Accepted: 02/17/2005] [Indexed: 02/07/2023]
Abstract
The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
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Affiliation(s)
- L. Eichinger
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - J.A. Pachebat
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - G. Glöckner
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - M.-A. Rajandream
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Sucgang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - M. Berriman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - R. Olsen
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - K. Szafranski
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - Q. Xu
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
| | - B. Tunggal
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - S. Kummerfeld
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - M. Madera
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - B. A. Konfortov
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - F. Rivero
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - A. T. Bankier
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - R. Lehmann
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - N. Hamlin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Davies
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P. Gaudet
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - P. Fey
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - K. Pilcher
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - G. Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - D. Saunders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - E. Sodergren
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Kerhornou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - X. Nie
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - N. Hall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - C. Anjard
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - L. Hemphill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - N. Bason
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P. Farbrother
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - B. Desany
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - E. Just
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - T. Morio
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - R. Rost
- Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - C. Churcher
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Cooper
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Haydock
- Biochemistry Department, University of Cambridge, Cambridge CB2 1QW, UK
| | - N. van Driessche
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - A. Cronin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - I. Goodhead
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - T. Mourier
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Pain
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Lu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - D. Harper
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R. Lindsay
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
| | - H. Hauser
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - K. James
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Quiles
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Madan Babu
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - T. Saito
- Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810 Japan
| | - C. Buchrieser
- Unité de Genomique des Microorganismes Pathogenes, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - A. Wardroper
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
- Department of Biology, University of York, York YO10 5YW, UK
| | - M. Felder
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - M. Thangavelu
- MRC Cancer Cell Unit, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, UK
| | - D. Johnson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Knights
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - H. Loulseged
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - K. Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - K. Oliver
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - C. Price
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M.A. Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - H. Urushihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - J. Hernandez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - E. Rabbinowitsch
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Steffen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Sanders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Ma
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Y. Kohara
- Centre for Genetic Resource Information, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - S. Sharp
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - M. Simmonds
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Spiegler
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Tivey
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S. Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato, Tokyo 108-8639, Japan
| | - B. White
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - D. Walker
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J. Woodward
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - T. Winckler
- Institut für Pharmazeutische Biologie, Universität Frankfurt (Biozentrum), Frankfurt am Main, 60439, Germany
| | - Y. Tanaka
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - G. Shaulsky
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston TX 77030, USA
| | - M. Schleicher
- Adolf-Butenandt-Institute/Cell Biology, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - G. Weinstock
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - A. Rosenthal
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - E.C. Cox
- Department of Molecular Biology, Princeton University, Princeton, NJ08544-1003, USA
| | - R. L. Chisholm
- dictyBase, Center for Genetic Medicine, Northwestern University, 303 E Chicago Ave, Chicago, IL 60611, USA
| | - R. Gibbs
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - W. F. Loomis
- Section of Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - M. Platzer
- Genome Analysis, Institute for Molecular Biotechnology, Beutenbergstr. 11, D-07745 Jena, Germany
| | - R. R. Kay
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - J. Williams
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - P. H. Dear
- Laboratory of Molecular Biology, MRC Centre, Cambridge CB2 2QH, UK
| | - A. A. Noegel
- Center for Biochemistry and Center for Molecular Medicine Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
| | - B. Barrell
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A. Kuspa
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030, USA
- Dept. of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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