Assumptions about genomic diversity may create conservation illusions of population health

Researchers at the University of Copenhagen have found that the critically endangered regent honeyeater faces hidden genetic risks while still retaining relatively high genetic diversity, risks that become apparent when combining genomic data across time with ecological modeling.

As global biodiversity continues to decline, one of the more subtle yet serious threats facing endangered species is genomic erosion, the gradual loss of genetic diversity within a population. This erosion weakens a species’ ability to adapt to environmental changes, increases the likelihood of inbreeding, and ultimately raises extinction risk.

While conservation efforts often focus on population numbers and visible threats like habitat loss, the genetic health of a species is equally important.

Key genetic indicators such as diversity, population structure, inbreeding, and effective population size are recognized as essential components of biodiversity monitoring. These metrics help scientists understand how populations are changing over time and how resilient they may be in the future.

But what if genetic erosion lags behind critical population decline? As a result, a species may still appear genetically healthy when viewed at a single point in time, even though its numbers have already dropped sharply. Without tracking genetic data across time, conservation assessments might miss early warning signs and underestimate long-term risks.

The regent honeyeater, a once-common songbird from southeastern Australia, is a powerful example of this hidden risk. Once widespread and abundant, the species has suffered steep declines due to habitat destruction, land clearing, and increased competition from other birds. Today, fewer than 250 mature individuals remain in the wild.

Despite this dramatic reduction in population, the regent honeyeater still shows relatively high genetic diversity in standard assessments. This unintuitive result makes it an ideal case for studying how genetic risks can be masked in species that have undergone recent declines.

In the study, “Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction,” published in Proceedings of the Royal Society B, researchers used whole-genome sequencing, ecological modeling, and forward-in-time simulations to understand how genetic erosion unfolds over time in the critically endangered regent honeyeater.

To examine how genetic erosion has progressed in the regent honeyeater, researchers sequenced the entire genomes of 44 individuals. This included 24 historical specimens collected before 1919 and 20 modern birds sampled between 2011 and 2016, providing a century-scale view of genetic change.

Modern DNA came from blood samples, while historical DNA was extracted from museum specimens using specialized methods optimized for degraded material. Sequencing reads were aligned to the genome of a closely related honeyeater species, reducing bias and ensuring comparability between time periods.

High-throughput analysis tools measured genome-wide heterozygosity, inbreeding levels, and population structure. Two demographic modeling approaches were used to reconstruct the species’ population history, capturing both long-term trends and recent shifts.

Species distribution models were built using historical occurrence data, land use, and climate variables spanning 1901 to 2015. These models mapped changes in environmental suitability over time and projected future scenarios based on different climate pathways.

Individual-based genomic simulations added a predictive component. By modeling populations with varying ancestral sizes and bottleneck intensities, the researchers estimated how genetic diversity and harmful mutations might evolve after a population collapse, revealing how genetic risks can remain hidden long after a population declines.

Genome comparisons between historical and modern regent honeyeaters revealed a modest but significant loss of genetic diversity. On average, modern individuals showed about a 9% reduction in genome-wide heterozygosity compared to historical samples.

This comparatively modest decline occurred during a greater than 99% reduction in population size over the same period, suggesting a time lag between demographic collapse and genetic erosion.

Principal component analysis showed clear genetic differences between historical and modern samples, though both sets of individuals remained part of a single, largely admixed population. Inbreeding levels were consistently low in both modern and historical individuals, and runs of homozygosity were short, suggesting that the species has so far avoided severe genetic isolation, likely due to its historically large and mobile population.

Species distribution models revealed a marked decline in environmental suitability across much of the regent honeyeater’s range over the last century. The most significant losses occurred in breeding habitats. Breeding habitat that remains suitable today is expected to decline rapidly, with the majority of that loss projected to occur before 2040.

High genetic diversity is often taken as a reassuring sign in conservation. In light of the current findings, that assumption can be entirely misleading.

Evidence from the regent honeyeater shows just how fragile that illusion can be. Even in populations that have crashed in number, genetic indicators may appear stable, concealing the early stages of long-term erosion. Without accounting for time-lag effects, critical risks can go unnoticed until it is too late to intervene.

These two timelines, slow-moving genomic erosion and rapid ecological deterioration, create a conservation challenge that cannot be addressed through either lens alone.

Combining historical genomic data with forward-looking environmental models uncovers risks that neither approach could fully reveal in isolation. By integrating both, the research highlights the urgency of early intervention and the need for long-term monitoring strategies that account for hidden genetic and ecological threats.

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