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Integrating habitat suitability modeling with gene flow improves delineation of landscape connections among African savanna elephants

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Abstract

Across Africa, space for conservation is sometimes limited to formally protected areas that have become progressively more isolated. There is a need for targeted conservation initiatives such as the demarcation of landscape connections, defined as areas that encompass environmental variables that promote the natural movement of individuals between populations, which can facilitate gene flow. Landscape connections can mitigate genetic isolation, genetic drift, and inbreeding, which can occur in isolated populations in protected areas. Promoting gene flow can reduce the risk of extirpation often associated with isolated populations. Here we develop and test models for identifying landscape connections among African savannah elephant (Loxodonta africana) populations by combining habitat suitability modeling with gene flow estimates across a large region including seven countries. We find a pronounced non-linear response to unsuitable habitat, consistent with previous studies showing that non-transformed habitat models are poor predictors of gene flow. We generated a landscape connections map that considers both suitable habitats based on telemetry occurrence data and gene flow estimated as the inverse of individual genetic distance, delineating areas that are important for maintaining elephant population connectivity. Our approach represents a novel framework for developing spatially and genetically informed conservation strategies for elephants and many other taxa distributed across heterogeneous and fragmented landscapes.

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Data availability

All bioinformatic code associated with this manuscript may be found at https://github.com/adeflamingh/de_Flamingh_et_al_Landscape_Connectivity and genetic data is available on DRYAD: https://doi.org/10.5061/dryad.qnk98sfp5. 

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Acknowledgements

We dedicate this paper to the memory of Rudi van Aarde whose life-long passion and dedication to conservation was and continues to be a driving force for the protection of Africa’s elephants. We thank Camilla Nørgaard for permission to include the late Rudi van Aarde as co-author. For facilitating sample collection, we thank Elephant Without Borders (Botswana) and the CERU team. The Zambian Wildlife Authority, the Department of Wildlife and National Parks (Botswana), South African National Parks (SANParks) and the Department of Agriculture, Forestry and Fisheries (South Africa) sanctioned the research. We acknowledge technical support provided by the University of Pretoria’s Sequencing Facility; the High-Throughput Sequencing and Genotyping Unit of the University of Illinois at Urbana-Champaign (UIUC); and the Illinois Campus Cluster, a computing resource that is operated by the Illinois Campus Cluster Program (ICCP) in conjunction with the National Center for Supercomputing Applications (NCSA) and which is supported by funds from UIUC.

Funding

For funding we thank the International Fund for Animal Welfare; the Conservation Ecology Research Unit (CERU) of the University of Pretoria; the Conservation Foundation (Zambia); the US Fish and Wildlife Service African Elephant Conservation Fund. In addition to support from these sources, AdF received a Francis M. and Harlie M. Clark Research Support Grant, a Harley J. Van Cleave Research Award, a University of Illinois Graduate College Dissertation Project Travel Grant, and support from the Cooperative State Research, Education, and Extension Service, US Department of Agriculture under project number ILLU 875–952.

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Authors and Affiliations

  1. Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA

    Alida de Flamingh & Alfred L. Roca

  2. Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana-Champaign, IL, USA

    Nathan Alexander & Robert L. Schooley

  3. Technology Transfer Office, Division of Research and Innovation, San Diego State University, San Diego, USA

    Tolulope I. N. Perrin-Stowe

  4. Peoria Zoo, Peoria, IL, USA

    Cassidy Donnelly

  5. Conservation Ecology Research Unit, Department of Zoology and Entomology, University of Pretoria, Pretoria, Gauteng, South Africa

    Robert A. R. Guldemond & Rudi J. van Aarde

  6. Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, USA

    Alfred L. Roca

Authors
  1. Alida de Flamingh
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  2. Nathan Alexander
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  3. Tolulope I. N. Perrin-Stowe
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  4. Cassidy Donnelly
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  5. Robert A. R. Guldemond
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  6. Robert L. Schooley
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  7. Rudi J. van Aarde
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  8. Alfred L. Roca
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Contributions

AdF, RLS, RJvA and ALR conceived and developed the methodological analysis approach. AdF, TINPS and CD completed the molecular work, and AdF and NA conducted the computational analyses. AdF wrote the original draft of the manuscript, all authors provided critical feedback throughout the process of interpretation of the data and of manuscript preparation, and approved of the final version of the manuscript.

Corresponding author

Correspondence to Alida de Flamingh.

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Competing interests

The authors have no relevant financial or non-financial interests to disclose.

Ethical approval

The Animal Ethics Committee of the University of Pretoria (AUCC-040611-013) and the Botswana Ministry of Environment, Wildlife, & Tourism (OP 46/1 LXXXV 89) reviewed and approved the telemetry collaring of the elephants. Collection and export/import of elephant dung was sanctioned by appropriate authorities prior to collection, including South African National Parks, the Department of Agriculture, Forestry and Fisheries in South Africa and the United States Department of Agriculture in the United States of America.

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Communicated by David Hawksworth.

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Deceased author: Rudi J. van Aarde

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Supplementary file1 (DOCX 5252 KB)

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de Flamingh, A., Alexander, N., Perrin-Stowe, T.I.N. et al. Integrating habitat suitability modeling with gene flow improves delineation of landscape connections among African savanna elephants. Biodivers Conserv 33, 3231–3252 (2024). https://doi.org/10.1007/s10531-024-02910-0

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