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Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery

Fontsere, Claudia ; Speak, Samuel A. ; Caven, Andrew J. ; Rodríguez, Juan Antonio ; Wang, Xuejing ; Pacheco, Carolina LU orcid ; Cassatt-Johnstone, Molly ; Femerling, Georgette ; Maloney, Brigid and Balacco, Jennifer , et al. (2025) In Molecular Ecology
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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
epub
subject
keywords
captive breeding, conservation genetics, genomic erosion, population genetics—empirical, whooping crane
in
Molecular Ecology
article number
e70088
publisher
Wiley-Blackwell
external identifiers
  • scopus:105014121129
  • pmid:40856093
ISSN
0962-1083
DOI
10.1111/mec.70088
language
English
LU publication?
yes
id
86235596-5b81-466b-b617-cf517afeced3
date added to LUP
2025-11-17 13:10:27
date last changed
2025-11-24 10:58:45
@article{86235596-5b81-466b-b617-cf517afeced3,
  abstract     = {{<p>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.</p>}},
  author       = {{Fontsere, Claudia and Speak, Samuel A. and Caven, Andrew J. and Rodríguez, Juan Antonio and Wang, Xuejing and Pacheco, Carolina and Cassatt-Johnstone, Molly and Femerling, Georgette and Maloney, Brigid and Balacco, Jennifer and Collins, Joanna and Sims, Ying and Abueg, Linelle and Fedrigo, Olivier and Jarvis, Erich D. and Hartup, Barry K. and Shapiro, Beth and Gilbert, M. Thomas P. and van Oosterhout, Cock and Morales, Hernán E.}},
  issn         = {{0962-1083}},
  keywords     = {{captive breeding; conservation genetics; genomic erosion; population genetics—empirical; whooping crane}},
  language     = {{eng}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Molecular Ecology}},
  title        = {{Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery}},
  url          = {{http://dx.doi.org/10.1111/mec.70088}},
  doi          = {{10.1111/mec.70088}},
  year         = {{2025}},
}