The genomic impact of population connectivity and decline in Africa’s elephants

African elephants are keystone species facing severe declines due to the ivory trade and habitat loss. To investigate the genomic consequences, we analyze 232 high-coverage genomes from 17 African countries in the first continent-wide genomic analysis treating savanna (Loxodonta africana) and forest (L. cyclotis) elephants as distinct species. We find a deep divergence between species, with forest elephants showing higher heterozygosity and historically larger effective population sizes, while savanna elephants exhibit greater inbreeding and genetic load. Surprisingly, we detect widespread introgression of trace forest ancestry across savanna populations, suggesting a complex history of hybridization. Within species, historically high mobility promoted genetic connectivity, though we identify signs of human-induced isolation and drift in peripheral populations. Our findings highlight gene flow as a key force in African elephant evolution and underscore the urgency of understanding the impact of accelerating habitat fragmentation in these ecosystem engineers.

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Publication Details

Journal
Nature Communications
Published
2026-04-16
DOI
https://doi.org/10.1038/s41467-026-71262-w
Primary Topic
Genetic diversity and population structure
Type
article
Field-Weighted Citation Impact
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article

The genomic impact of population connectivity and decline in Africa’s elephants

Cindy G. Santander, Nicholas J. Georgiadis, Rasmus Heller, Mrinalini Watsa et al.
Nature Communications
Genetic diversity and population structure
article

The genomic impact of population connectivity and decline in Africa’s elephants

Cindy G. Santander, Nicholas J. Georgiadis, Rasmus Heller, Mrinalini Watsa, Savanah Bird, Hans R. Siegismund, Laura D. Bertola, Christina Hvilsom, Chris Thouless, Ripan S. Malhi, Renzo F. Balboa, Stéphanie Bourgeois, Vincent B. Muwanika, Yasuko Ishida, Charles Masembe, Anubhab Khan, Patrícia Pečnerová, Karine A. Viaud‐Martinez, Mikkel Schubert, George Wittemyer, Kan Nobuta, Nelson Ting, Alida de Flamingh, Anna Brüniche–Olsen, Genís Garcia‐Erill, Amal Al‐Chaer, Sasha Treadup, Xiaodong Liu, Long Lin, Sylwia Urbaniak, Lauren M. Hennelly, Alfred L. Roca, Iain Douglas-Hamilton, Malthe S. Rasmussen, Xi Wang, Martin N. Tchamba, Peter J. Van Coeverden de Groot
article en

Abstract

African elephants are keystone species facing severe declines due to the ivory trade and habitat loss. To investigate the genomic consequences, we analyze 232 high-coverage genomes from 17 African countries in the first continent-wide genomic analysis treating savanna (Loxodonta africana) and forest (L. cyclotis) elephants as distinct species. We find a deep divergence between species, with forest elephants showing higher heterozygosity and historically larger effective population sizes, while savanna elephants exhibit greater inbreeding and genetic load. Surprisingly, we detect widespread introgression of trace forest ancestry across savanna populations, suggesting a complex history of hybridization. Within species, historically high mobility promoted genetic connectivity, though we identify signs of human-induced isolation and drift in peripheral populations. Our findings highlight gene flow as a key force in African elephant evolution and underscore the urgency of understanding the impact of accelerating habitat fragmentation in these ecosystem engineers.

Nature CommunicationsVol. 17(1)
University of Copenhagen (DK), Zoological Society of San Diego (US), University of Illinois Urbana-Champaign (US), Université de Dschang (CM), Illumina (United States) (US), University of Oregon (US), Urbana University (US), Save the Elephants (KE), Lund University (SE), National Centre for Biological Sciences (IN), Aarhus University (DK), Queen's University (CA), Smithsonian Conservation Biology Institute (US), Novo Nordisk Foundation (DK), Copenhagen Zoo (DK), National Zoological Park (US), St. Anthony Hospital (US), National Agency for National Parks (GA), Digital Research Alliance of Canada, Conservation Biology Institute, Indian Institute of Science Bangalore (IN), Makerere University (UG), Rice University (US), Colorado State University (US)
National Science Foundation, Smithsonian Institution, L'Oreal USA, National Geographic Society, Colorado State University, Indian Institute of Science, Rice University, University of Oregon, European Commission, Svenska Forskningsrådet Formas, Lunds Universitet, Queen's University, Novo Nordisk, Agence Nationale Des Parcs Nationaux, Faculty of Health and Medical Sciences, University of Western Australia, Novo Nordisk Foundation Center for Basic Metabolic Research, U.S. Fish and Wildlife Service, University of Illinois at Urbana-Champaign, Smithsonian Conservation Biology Institute, Horizon 2020 Framework Programme, Det Sundhedsvidenskabelige Fakultet, Københavns Universitet
Life in Land
Openalex Percentile: Top 26%
Genetic diversity and population structure
DOIOpen Access PDFOpenAlex
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