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

Pečnerová, Patrícia LU orcid ; Ishida, Yasuko ; Garcia-Erill, Genís ; Bertola, Laura D. ; Santander, Cindy G. ; Liu, Xiaodong ; Brüniche-Olsen, Anna ; Khan, Anubhab ; Hennelly, Lauren M. and Balboa, Renzo F. , et al. (2026) In Nature Communications 17(1).
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... (More)

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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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Nature Communications
volume
17
issue
1
article number
3223
publisher
Nature Publishing Group
external identifiers
  • scopus:105035818738
  • pmid:41991514
ISSN
2041-1723
DOI
10.1038/s41467-026-71262-w
language
English
LU publication?
yes
id
8c10afb4-2142-4a02-93f1-9ce4ce8bb5fc
date added to LUP
2026-06-24 09:00:20
date last changed
2026-06-29 15:17:35
@article{8c10afb4-2142-4a02-93f1-9ce4ce8bb5fc,
  abstract     = {{<p>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.</p>}},
  author       = {{Pečnerová, Patrícia and Ishida, Yasuko and Garcia-Erill, Genís and Bertola, Laura D. and Santander, Cindy G. and Liu, Xiaodong and Brüniche-Olsen, Anna and Khan, Anubhab and Hennelly, Lauren M. and Balboa, Renzo F. and Lin, Long and Rasmussen, Malthe S. and Wang, Xi and Schubert, Mikkel and Al-Chaer, Amal and Urbaniak, Sylwia and Nobuta, Kan and Treadup, Sasha and Viaud-Martinez, Karine A. and de Flamingh, Alida and Malhi, Ripan S. and Bird, Savanah and Ting, Nelson and Watsa, Mrinalini and Tchamba, Martin N. and Bourgeois, Stéphanie and Thouless, Chris and Douglas-Hamilton, Iain and Wittemyer, George and Van Coeverden de Groot, Peter J. and Muwanika, Vincent B. and Masembe, Charles and Georgiadis, Nicholas J. and Hvilsom, Christina and Heller, Rasmus and Siegismund, Hans Redlef and Roca, Alfred L.}},
  issn         = {{2041-1723}},
  language     = {{eng}},
  month        = {{04}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature Communications}},
  title        = {{The genomic impact of population connectivity and decline in Africa’s elephants}},
  url          = {{http://dx.doi.org/10.1038/s41467-026-71262-w}},
  doi          = {{10.1038/s41467-026-71262-w}},
  volume       = {{17}},
  year         = {{2026}},
}