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Long-term biotic homogenization in the East African Rift System over the last 6 million years of hominin evolution

Nature Ecology & Evolution volume 8, pages 1751–1759 (2024)Cite this article

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Abstract

Eastern Africa preserves the most complete record of human evolution anywhere in the world but we have little knowledge of how long-term biogeographic dynamics in the region influenced hominin diversity and distributions. Here, we use spatial beta diversity analyses of mammal fossil records from the East African Rift System to reveal long-term biotic homogenization (increasing compositional similarity of faunas) over the last 6 Myr. Late Miocene and Pliocene faunas (~6–3 million years ago (Ma)) were largely composed of endemic species, with the shift towards biotic homogenization after ~3 Ma being driven by the loss of endemic species across functional groups and a growing number of shared grazing species. This major biogeographic transition closely tracks the regional expansion of grass-dominated ecosystems. Although grazers exhibit low beta diversity in open environments of the Early Pleistocene, the high beta diversity of Mio-Pliocene browsers and frugivores occurred in the context of extensive woody vegetation. We identify other key aspects of the Late Cenozoic biogeographic development of eastern Africa, their likely drivers and place the hominin fossil record in this context. Because hominins were undoubtedly influenced by many of the same factors as other eastern African mammals, this provides a new perspective on the links between environmental and human evolutionary histories.

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Fig. 1: Fossil and paleoenviromental data from the EARS and study predictions.
Fig. 2: Temporal trend in multisite Simpson dissimilarity (βSIM) for eastern African mammal species over the last 6 Myr.
Fig. 3: Biogeographic evolution of eastern African mammal faunas over the last 6 Myr.
Fig. 4: The contribution of shared versus endemic species in driving the biogeographic evolution of eastern African mammal faunas over the last 6 Myr.

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Data availability

All data generated or analysed during this study are provided on Zenodo via https://zenodo.org/records/11187857 (ref. 85).

Code availability

All code used for main text analyses is provided on Zenodo via https://zenodo.org/records/11187857 (ref. 85).

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Acknowledgements

This study was funded by NSF grants BCS 1551799 (to J.M.K.), BCS 1551810 (to K.E.R.) and a Darwin Postdoctoral Fellowship at the University of Massachusetts Amherst (to J.R.). A.D. thanks Colorado State University Vice President for Research office for funding. I.A.L. acknowledges funding from Ministerio de Ciencia e Innovación de España under grant no. RYC2021-034991-I, funded by MCIN/AEI/10.13039/501100011033 and European Union NextGenerationEU/PRTR. We thank T. M. Smiley and K. T. Uno for feedback, and C. M. Rowan for discussion of EARS tectonic evolution. C. M. Rowan helped to generate the map in Fig. 1.

Author information

Authors and Affiliations

  1. Department of Archaeology, University of Cambridge, Cambridge, UK

    John Rowan

  2. Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA

    Andrew Du

  3. Centre for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University, Aarhus, Denmark

    Erick J. Lundgren

  4. Department of Anthropology, University of Utah, Salt Lake City, UT, USA

    J. Tyler Faith

  5. Natural History Museum of Utah, University of Utah, Salt Lake City, UT, USA

    J. Tyler Faith

  6. Origins Centre, University of the Witwatersrand, Johannesburg, South Africa

    J. Tyler Faith

  7. Department of Biosciences, Rice University, Houston, TX, USA

    Lydia Beaudrot

  8. Program in Ecology and Evolutionary Biology, Rice University, Houston, TX, USA

    Lydia Beaudrot

  9. Department of Integrative Biology, Michigan State University, East Lansing, MI, USA

    Lydia Beaudrot

  10. Institute of Human Origins, Arizona State University, Tempe, AZ, USA

    Christopher J. Campisano & Kaye E. Reed

  11. School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA

    Christopher J. Campisano & Kaye E. Reed

  12. Naturalis Biodiversity Center, Leiden, the Netherlands

    Josephine C. Joordens

  13. Faculty of Archaeology, Leiden University, Leiden, the Netherlands

    Josephine C. Joordens

  14. Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands

    Josephine C. Joordens

  15. Faculty of Science and Engineering, Maastricht University, Maastricht, the Netherlands

    Josephine C. Joordens

  16. CENIEH (National Research Center on Human Evolution), Burgos, Spain

    Ignacio A. Lazagabaster

  17. Department of Evolution, Ecology & Behaviour, University of Liverpool, Liverpool, UK

    Ignacio A. Lazagabaster

  18. Department of Anatomy, Idaho College of Osteopathic Medicine, Idaho, ID, USA

    Ellis M. Locke

  19. Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, Lewisburg, WV, USA

    Irene E. Smail

  20. Department of Anthropology, University of Massachusetts Amherst, Amherst, MA, USA

    Jason M. Kamilar

  21. Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, USA

    Jason M. Kamilar

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Contributions

J.R. designed the research and compiled the data. J.R. and A.D. analysed the data. J.R., A.D., E.J.L., J.T.F., L.B., C.J.C., J.C.J, I.A.L., E.M.L., I.E.S, K.E.R. and J.M.K. contributed to the interpretation of results. J.R. wrote the manuscript with input from all authors. J.M.K. and K.E.R. secured the primary funding for this study with contributions from L.B.

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Correspondence to John Rowan.

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Extended data

Extended Data Fig. 1 Overview of analytical workflow used to generate main text results.

Main text (Figs. 2–4 and generated values reported in Supplementary Dataset 1) and sensitivity analyses (results reported in Extended Data Figs. 2–5, Supplementary Table 1 and generated values reported in Supplementary Dataset 1) are shown. Each step of the analysis is outlined, with schematic data plots illustrating examples of where the results of each analytical step are presented.

Extended Data Fig. 2 Sensitivity analysis for time bin starting age.

a) Our main text analyses of multisite Simpson dissimilarity (βSIM) used 500-kyr time bins starting at 6 Ma (6-5.5 Ma, 5.5-5 Ma…), but shifting the bin start age by 100-kyr increments (6-5.5 Ma, 5.9-5.4 Ma, 5.8-5.3 Ma, 5.7-5.2 Ma, 5.6-5.1 Ma) does not change the overall pattern. b) Temporal trend in multisite Simpson dissimilarity (βSIM) for eastern African mammal species over the last 6 Myr using our main text dataset (PA Matrix v1) and alternate versions of the dataset that with different treatments of open nomenclature; all four presence-absence matrices are included in Supplementary Dataset 1.

Extended Data Fig. 3 Raw sampling of the East African Rift System fossil record based on PA Matrix v1.

Measures include the number of sites per time bin, number of species per time bin and the average number of species per site by time bin.

Extended Data Fig. 4 Multisite Simpson dissimilarity (βSIM) in relation to sampling measures.

Scatterplots of our multisite Simpson dissimilarity (βSIM) for the overall East African Rift System trend by (a) number of species per time bin, (b) number of sites per time bin and (c) the average number of species per site by time bin. Correlations were assessed with a linear model using the lm() function in R.

Extended Data Fig. 5 Multisite Simpson dissimilarity (βSIM) in relation to sampling measures by functional group.

Scatterplots of our multisite Simpson dissimilarity (βSIM) for each diet and body size class functional group by number of (a) species per time bin, (b) number of sites per time bin and (c) the average number of species per site by time bin. All correlations, except for number of species for s1 taxa (see SI text) are weak and non-significant (see Supplementary Table 1).

Supplementary information

Supplementary Information

Supplementary Discussion and Table 1.

Reporting Summary

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Supplementary Code

R code used for analyses.

Supplementary Data

Dataset containing all raw and generated values for analyses.

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Rowan, J., Du, A., Lundgren, E.J. et al. Long-term biotic homogenization in the East African Rift System over the last 6 million years of hominin evolution. Nat Ecol Evol 8, 1751–1759 (2024). https://doi.org/10.1038/s41559-024-02462-0

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