Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction
(2025) In Proceedings of the Royal Society B: Biological Sciences 292(2043).- Abstract
Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-Time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-Temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years.... (More)
Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-Time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-Temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-Time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.
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- author
- Liu, Xufen ; Milesi, Ester ; Fontsere, Claudia ; Owens, Hannah L. ; Heinsohn, Robert ; Gilbert, M. Thomas P. ; Crates, Ross ; Nogués-Bravo, David and Morales, Hernán E. LU
- organization
- publishing date
- 2025-03
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- conservation, extinction, genetic diversity, genetic load, genomic erosion, genomics
- in
- Proceedings of the Royal Society B: Biological Sciences
- volume
- 292
- issue
- 2043
- article number
- 20242480
- publisher
- Royal Society Publishing
- external identifiers
-
- pmid:40132633
- scopus:105001511990
- ISSN
- 0962-8452
- DOI
- 10.1098/rspb.2024.2480
- language
- English
- LU publication?
- yes
- id
- b1516971-c6da-4131-9fa6-bad39b06e71d
- date added to LUP
- 2025-08-19 14:11:53
- date last changed
- 2025-08-19 14:12:33
@article{b1516971-c6da-4131-9fa6-bad39b06e71d,
abstract = {{<p>Global biodiversity is rapidly declining due to habitat degradation and genomic erosion, highlighting the urgent need to monitor endangered species and their genetic health. Temporal genomics and ecological modelling offer finer resolution than single-Time-point measurements, providing a comprehensive view of species' recent and future trajectories. We investigated genomic erosion and environmental suitability in the critically endangered regent honeyeater (Anthochaera phrygia) by sequencing whole genomes of historical and modern specimens and building multi-Temporal species distribution models (SDMs) across the last century. The species has declined from hundreds of thousands of individuals to fewer than 300 over the past 100 years. SDMs correctly predicted known patterns of local extinction in southeast Australia. Our demographic reconstructions revealed a gradual population decline from 2000 to 2500 years ago, sharply accelerating in the last 500 years due to climate variability and habitat loss. Despite this substantial demographic collapse, the regent honeyeater has lost only 9% of its genetic diversity, with no evidence of inbreeding or connectivity loss. Also, it exhibits higher diversity than many other threatened bird species. Forward-in-Time genomic simulations indicate that this time lag between population decline and genetic diversity loss conceals the risk of ongoing genomic erosion into a future of rapidly degrading environmental suitability. Our work underscores the need for targeted conservation efforts and continuous genetic monitoring to prevent species extinction.</p>}},
author = {{Liu, Xufen and Milesi, Ester and Fontsere, Claudia and Owens, Hannah L. and Heinsohn, Robert and Gilbert, M. Thomas P. and Crates, Ross and Nogués-Bravo, David and Morales, Hernán E.}},
issn = {{0962-8452}},
keywords = {{conservation; extinction; genetic diversity; genetic load; genomic erosion; genomics}},
language = {{eng}},
number = {{2043}},
publisher = {{Royal Society Publishing}},
series = {{Proceedings of the Royal Society B: Biological Sciences}},
title = {{Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction}},
url = {{http://dx.doi.org/10.1098/rspb.2024.2480}},
doi = {{10.1098/rspb.2024.2480}},
volume = {{292}},
year = {{2025}},
}