• A Corrigendum to this article was published on 24 August 2016

This article has been updated


Understanding how ecological communities are organized and how they change through time is critical to predicting the effects of climate change1. Recent work documenting the co-occurrence structure of modern communities found that most significant species pairs co-occur less frequently than would be expected by chance2,3. However, little is known about how co-occurrence structure changes through time. Here we evaluate changes in plant and animal community organization over geological time by quantifying the co-occurrence structure of 359,896 unique taxon pairs in 80 assemblages spanning the past 300 million years. Co-occurrences of most taxon pairs were statistically random, but a significant fraction were spatially aggregated or segregated. Aggregated pairs dominated from the Carboniferous period (307 million years ago) to the early Holocene epoch (11,700 years before present), when there was a pronounced shift to more segregated pairs, a trend that continues in modern assemblages. The shift began during the Holocene and coincided with increasing human population size4,5 and the spread of agriculture in North America6,7. Before the shift, an average of 64% of significant pairs were aggregated; after the shift, the average dropped to 37%. The organization of modern and late Holocene plant and animal assemblages differs fundamentally from that of assemblages over the past 300 million years that predate the large-scale impacts of humans. Our results suggest that the rules governing the assembly of communities have recently been changed by human activity.

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Change history

  • 06 January 2016

    ED Table 1 was corrected (specifically the data owner for Wisconsin plant data).


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We thank G. Dietl for comments that improved the manuscript. Support for this research was provided by a National Museum of Natural History Program grant to the Evolution of Terrestrial Ecosystems Program (ETE) and NSF-DEB 1257625. This is ETE publication 338.

Author information


  1. Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, USA

    • S. Kathleen Lyons
    • , Anna K. Behrensmeyer
    • , Antoine Bercovici
    • , Matt Davis
    • , William A. DiMichele
    • , Conrad Labandeira
    • , Anikó Tóth
    •  & Scott Wing
  2. Department of Environmental Science and Biology, The College at Brockport – SUNY, Brockport, New York 14420, USA

    • Kathryn L. Amatangelo
  3. School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343, USA

    • Jessica L. Blois
  4. Department of Geology and Geophysics, Yale University, New Haven, Connecticut 06520, USA

    • Matt Davis
  5. Hominid Paleobiology Doctoral Program, Center for the Advanced Study of Hominid Paleobiology, Department of Anthropology, George Washington University, Washington DC 20052, USA

    • Andrew Du
    • , David Patterson
    •  & Amelia Villaseñor
  6. Department of Geosciences and Geography, University of Helsinki, PO Box 64, 00014 University of Helsinki, Finland

    • Jussi T. Eronen
  7. School of Social Science, The University of Queensland, Brisbane, Queensland 4072, Australia

    • J. Tyler Faith
  8. Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, USA

    • Gary R. Graves
  9. Center for Macroecology, Evolution and Climate, University of Copenhagen, Copenhagen 2100, Denmark

    • Gary R. Graves
  10. Biological Sciences Graduate Program, University of Maryland, College Park, Maryland 20742, USA

    • Nathan Jud
  11. Florida Museum of Natural History, University of Florida, Gainsville, Florida 32611, USA

    • Nathan Jud
  12. Department of Entomology, University of Maryland College Park, College Park, Maryland 20742, USA

    • Conrad Labandeira
  13. Key Lab of Insect Evolution and Environmental Changes, Capital Normal University, Beijing 100048, China

    • Conrad Labandeira
  14. Department of Integrative Biology and Museum of Paleontology, University of California Berkeley, Berkeley, California 94720, USA

    • Cindy V. Looy
  15. School Biology and Ecology & Sustainability Solutions Initiative, University of Maine, Orono, Maine 04469, USA

    • Brian McGill
  16. Department of Geology, University of Cincinnati, Cincinnati, Ohio 45221, USA

    • Joshua H. Miller
  17. Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia

    • Silvia Pineda-Munoz
  18. Department of Anthropology, Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington DC 20013, USA

    • Richard Potts
  19. School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, Nevada 89154, USA

    • Brett Riddle
  20. Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331, USA

    • Rebecca Terry
  21. Chair of Ecology and Biogeography, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland

    • Werner Ulrich
  22. Evolutionary Studies Institute, University of the Witwatersrand, Jorissen Street, Braamfontein, Johannesburg 2001, South Africa

    • Heidi Anderson
    •  & John Anderson
  23. Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

    • Donald Waller
  24. Department of Biology, University of Vermont, Burlington, Vermont 05405, USA

    • Nicholas J. Gotelli


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All authors provided input into the final manuscript. S.K.L. helped design the study, contributed and analysed data, and wrote the paper. K.L.A., J.L.B., J.T.F., and W.U. were involved in the study design, and contributed and analysed data. A.T. was involved in the study design, contributed and analysed data, and created Supplementary Fig. 1. A.K.B., A.B., W.A.D., J.T.E., N.J., C.L., C.V.L., S.W., and B.R. were involved in the study design and contributed data. H.A., J.A., and D.W. contributed data. M.D. and J.H.M. were involved in the study design, analysed data, created figures and wrote text for the supplementary information. A.D. was involved in the study design and analysed data. G.R.G., B.M., D.P., S.P.-M., R.T., R.P., and A.V. were involved in the study design. N.J.G. designed the study and helped write the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to S. Kathleen Lyons.

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    Supplementary Information

    This file contains Supplementary Text and Data comprising: Dataset criteria, Modern data; Matrix Fill; Mammal Datasets; Plant Datasets.

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