Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery

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.

Authors

Institutions

Publication Details

Journal
Molecular Ecology
Published
2025-08-26
DOI
https://doi.org/10.1111/mec.70088
Citations
5
Primary Topic
Genetic diversity and population structure
Type
article
Field-Weighted Citation Impact
9.09

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery

Hernán E. Morales, Claudia Fontsere, Molly Cassatt‐Johnstone, Erich D. Jarvis et al.
5 citations
Molecular Ecology
Genetic diversity and population structure
9.09
article

Persistent Genomic Erosion in Whooping Cranes Despite Demographic Recovery

Hernán E. Morales, Claudia Fontsere, Molly Cassatt‐Johnstone, Erich D. Jarvis, Jennifer Balacco, Andrew J. Caven, Linelle Ann L. Abueg, Samuel A. Speak, Beth Shapiro, Marcus Thomas P. Gilbert, Olivier Fédrigo, Georgette Femerling, Carolina Pacheco, Cock van Oosterhout, Joanna Collins, Brigid Maloney, Barry K. Hartup, Ying Sims, Xuejing Wang, Juan Antonio Rodríguez
article en
5 citations

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.

Molecular EcologyVol. 34(23)
University of East Anglia (GB), University of Copenhagen (DK), Natural History Museum (GB), University of Wisconsin–Madison (US), University of California, Santa Cruz (US), Lund University (SE), Chester Zoo (GB), International Crane Foundation (US), Vitensenteret i Trondheim (NO), Cranfield Trust (GB), McGill University (CA), Rockefeller University (US)
Howard Hughes Medical Institute, James Hutton Institute, European Commission, National Research Foundation, Danmarks Grundforskningsfond, Chester Zoo, Directorate for Biological Sciences, U.S. Fish and Wildlife Service, U.S. Geological Survey, Biotechnology and Biological Sciences Research Council, Natural Environment Research Council, Research Executive Agency, H2020 European Research Council
Openalex Percentile: Top 2%
Genetic diversity and population structure
9.09
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.