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Fontsere, Claudia, Speak, Samuel A. 
ORCID: https://orcid.org/0000-0002-4207-7562, Caven, Andrew J., Rodríguez, Juan Antonio, Wang, Xuejing, Pacheco, Carolina, Cassatt-Johnstone, Molly, Femerling, Georgette, Maloney, Brigid, Balacco, Jennifer, Collins, Joanna, Sims, Ying, Abueg, Linelle, Fedrigo, Olivier, Jarvis, Erich D., Hartup, Barry K., Shapiro, Beth, Gilbert, M. Thomas P., van Oosterhout, Cock ORCID: https://orcid.org/0000-0002-5653-738X and Morales, Hernán E.
(2025)
Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery.
Molecular Ecology, 34 (23).
ISSN 0962-1083
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Abstract
Integrating in-situ (wild) and ex-situ (captive) conservation efforts can mitigate genetic diversity loss and help prevent extinction of endangered wild populations. The whooping crane (Grus americana) experienced severe population declines in the 18th century, culminating in a collapse to ~20 individuals by 1944. Legal protections and conservation actions have since increased the census population from a stock of 16 individuals to approximately 840 individuals, yet the impact on genomic diversity remains unclear. We analysed the temporal dynamics of genomic erosion by sequencing a high-quality reference genome, and re-sequencing 16 historical (years 1867–1893) and 37 modern (2007–2020) genomes, including wild individuals and four generations of captive-bred individuals. Genomic demographic reconstructions reveal a steady decline, accelerating over the past 300 years with the European settlement of North America. Temporal genomic analyses show that despite demographic recovery, the species has lost 70% of its historical genetic diversity and has increased its inbreeding. Although the modern population bottleneck reduced the ancestral genetic load, modern populations possess more realised load than masked load, possibly resulting in a chronic loss of fitness. Integrating pedigree and genomic data, we underscore the role of breeding management in reducing recent inbreeding. Yet ongoing heterozygosity loss, load accumulation, and persistent effects of historical inbreeding (i.e., background inbreeding) argue against the species' downlisting from its current Endangered status on the IUCN Red List and the Endangered Species Act. The presence of private genetic variation in wild and captive populations suggests that wild-captive crosses could enhance genetic diversity and reduce the realised load. Our findings emphasise the role of genomics in informing conservation management and policy.
| Item Type: | Article |
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| Additional Information: | Data Availability Statement: All raw data generated in this study has been uploaded to the EuropeanNucleotide Archive (ENA; Accession no. PRJEB80530). The metadataof these samples can be found in Table S2. Code for data analysis canbe accessed through GitHub: https://github.com/claudefa/ WhoopingCrane_ genomics, https://github.com/pollicipes/ROHbin and https://github.com/saspeak/LoadLift. |
| Uncontrolled Keywords: | captive breeding,conservation genetics,genomic erosion,population genetics—empirical,whooping crane,ecology, evolution, behavior and systematics,genetics ,/dk/atira/pure/subjectarea/asjc/1100/1105 |
| Faculty \ School: | Faculty of Science > School of Environmental Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 10 Aug 2026 14:37 |
| Last Modified: | 11 Aug 2026 12:41 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/104092 |
| DOI: | 10.1111/mec.70088 |
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