Genomics Reveals Distinct Evolutionary Lineages in Asian Elephants
ABSTRACT This study introduces, for the first time, whole‐genome sequencing (WGS) data from predominantly wild‐born Asian elephants currently housed in European zoos, covering the distribution range of Asian elephants. With this WGS data, we aim to validate the current designation of Asian elephant...
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| Format: | Article |
| Language: | English |
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Wiley
2025-08-01
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| Series: | Ecology and Evolution |
| Online Access: | https://doi.org/10.1002/ece3.72019 |
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| author | Jeroen Kappelhof Emma Diepeveen Martijn F. L. Derks Ole Madsen Rebekah Rogers Benoit Goossens Reeta Sharma Martien A. M. Groenen Jack J. Windig Mirte Bosse |
| author_facet | Jeroen Kappelhof Emma Diepeveen Martijn F. L. Derks Ole Madsen Rebekah Rogers Benoit Goossens Reeta Sharma Martien A. M. Groenen Jack J. Windig Mirte Bosse |
| author_sort | Jeroen Kappelhof |
| collection | DOAJ |
| description | ABSTRACT This study introduces, for the first time, whole‐genome sequencing (WGS) data from predominantly wild‐born Asian elephants currently housed in European zoos, covering the distribution range of Asian elephants. With this WGS data, we aim to validate the current designation of Asian elephant subspecies and address currently discussed ambiguities about their origin, particularly concerning Bornean and Sri Lankan elephants by analyzing population structure, determining divergence times, and exploring ancient and recent bottlenecks. Understanding the evolutionary history of the Asian elephant subspecies is essential for developing targeted conservation strategies and mitigating risks to their survival. Analysis reveals a clear population structure with relatively recent splits, delineating three distinct genetic clusters: Borneo, Sumatra, and Asian Mainland, with Sri Lanka forming an additional group. We estimated the divergence time between Bornean and Sumatran elephants to be around 170,000 years ago. The divergence of the Sri Lankan elephant from the Mainland is estimated to have occurred around 48,000 years ago, with Sri Lankan elephants predominantly clustering with those from Myanmar, possibly due to historical trade networks. The genome of the Bornean elephant exhibited signatures of severe bottlenecks as recently as 8 and 38 generations ago, further supporting hypotheses of their introduction. Our data reflect the current Asian elephant subspecies designation. Additionally, for the first time, the Sumatra elephant is confirmed as a distinct subspecies with genomic data. Furthermore, the study discusses genetic management strategies for ex‐situ populations, emphasizing the importance of implementing cluster‐specific conservation measures. |
| format | Article |
| id | doaj-art-bdbb38bb321744968199fa778339d0e5 |
| institution | Kabale University |
| issn | 2045-7758 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecology and Evolution |
| spelling | doaj-art-bdbb38bb321744968199fa778339d0e52025-08-20T03:44:09ZengWileyEcology and Evolution2045-77582025-08-01158n/an/a10.1002/ece3.72019Genomics Reveals Distinct Evolutionary Lineages in Asian ElephantsJeroen Kappelhof0Emma Diepeveen1Martijn F. L. Derks2Ole Madsen3Rebekah Rogers4Benoit Goossens5Reeta Sharma6Martien A. M. Groenen7Jack J. Windig8Mirte Bosse9Animal Breeding and Genomics Wageningen University and Research Wageningen the NetherlandsA‐LIFE, Section Ecology & Evolution Vrije Universiteit Amsterdam Amsterdam the NetherlandsAnimal Breeding and Genomics Wageningen University and Research Wageningen the NetherlandsAnimal Breeding and Genomics Wageningen University and Research Wageningen the NetherlandsDepartment of Bioinformatics and Genomics University of North Carolina Charlotte North Carolina USADanau Girang Field Centre C/o Sabah Wildlife Department Kota Kinabalu Sabah MalaysiaRoyal Rotterdam Zoological & Botanical Gardens Rotterdam the NetherlandsAnimal Breeding and Genomics Wageningen University and Research Wageningen the NetherlandsAnimal Breeding and Genomics Wageningen University and Research Wageningen the NetherlandsAnimal Breeding and Genomics Wageningen University and Research Wageningen the NetherlandsABSTRACT This study introduces, for the first time, whole‐genome sequencing (WGS) data from predominantly wild‐born Asian elephants currently housed in European zoos, covering the distribution range of Asian elephants. With this WGS data, we aim to validate the current designation of Asian elephant subspecies and address currently discussed ambiguities about their origin, particularly concerning Bornean and Sri Lankan elephants by analyzing population structure, determining divergence times, and exploring ancient and recent bottlenecks. Understanding the evolutionary history of the Asian elephant subspecies is essential for developing targeted conservation strategies and mitigating risks to their survival. Analysis reveals a clear population structure with relatively recent splits, delineating three distinct genetic clusters: Borneo, Sumatra, and Asian Mainland, with Sri Lanka forming an additional group. We estimated the divergence time between Bornean and Sumatran elephants to be around 170,000 years ago. The divergence of the Sri Lankan elephant from the Mainland is estimated to have occurred around 48,000 years ago, with Sri Lankan elephants predominantly clustering with those from Myanmar, possibly due to historical trade networks. The genome of the Bornean elephant exhibited signatures of severe bottlenecks as recently as 8 and 38 generations ago, further supporting hypotheses of their introduction. Our data reflect the current Asian elephant subspecies designation. Additionally, for the first time, the Sumatra elephant is confirmed as a distinct subspecies with genomic data. Furthermore, the study discusses genetic management strategies for ex‐situ populations, emphasizing the importance of implementing cluster‐specific conservation measures.https://doi.org/10.1002/ece3.72019 |
| spellingShingle | Jeroen Kappelhof Emma Diepeveen Martijn F. L. Derks Ole Madsen Rebekah Rogers Benoit Goossens Reeta Sharma Martien A. M. Groenen Jack J. Windig Mirte Bosse Genomics Reveals Distinct Evolutionary Lineages in Asian Elephants Ecology and Evolution |
| title | Genomics Reveals Distinct Evolutionary Lineages in Asian Elephants |
| title_full | Genomics Reveals Distinct Evolutionary Lineages in Asian Elephants |
| title_fullStr | Genomics Reveals Distinct Evolutionary Lineages in Asian Elephants |
| title_full_unstemmed | Genomics Reveals Distinct Evolutionary Lineages in Asian Elephants |
| title_short | Genomics Reveals Distinct Evolutionary Lineages in Asian Elephants |
| title_sort | genomics reveals distinct evolutionary lineages in asian elephants |
| url | https://doi.org/10.1002/ece3.72019 |
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