image: The honeybee collection at the Paris Museum of Natural History from 1865–1919
Credit: ©Science China Press
Insect population declines have now received considerable public, and scientific attention with a recent “special issue in Nature” (volume 628 Issue 8007) covering the environmental challenges facing insect populations with metadata synthesized from 106 studies or continuous biomonitoring datasets assessing trends in insect abundance spanning 16-27 years. However, abundance per se cannot fully inform species’ health - a prime example comes from multifarious crops and stock animals, which may face long-term sustainability challenges, despite their large population sizes. Furthermore, long-term monitoring datasets with repeatable sampling methods are rarely available for insects, further increasing uncertainties about current status. Genetic information preserved within museum specimens acts as a historical record, reflecting the genetic makeup of target species and their populations during specific historical periods. This provides invaluable historical data for analyzing the impact of recent human activities on populations. The sheer volume of insect museum specimens — far greater than other taxonomic groups — gives them a significant advantage in dissecting the influence of recent anthropogenic changes.
Based on this, a collaborative research team — involving the Institute of Zoology, Chinese Academy of Sciences (CAS), China Agricultural University, the University of Copenhagen (Denmark), and other institutions — turned its attention to these "time archives": centuries-old historical museum specimens.
Reading Precious Historical Information from Museum Specimens
The research team acquired 46 specimens of the Asian honeybee (Apis cerana) dating back approximately 120 years and performed whole-genome comparison with 352 modern samples. The samples covered the primary geographical populations of A. cerana. According to records of the Chinese National Animal Collection Resource Center, only a single A. cerana specimen reaches to this age. This rarity underscores the significance of the genomic datasets, positioning this study as one of the first systematic museomic investigations in non-model insect species. The results showed that although the main A. cerana lineages did not disappear over the century, the genetic diversity of their core populations significantly declined. In other words, even if population numbers may be stable, their "genetic health" is quietly deteriorating. This drop in genetic diversity suggests that the honeybees' ability to cope with future climate change and environmental pressures may be weakening.
Pesticides: The Invisible Force Driving Rapid Honeybee Evolution
The team further analyzed the SNP loci that underwent significant temporal shifts in allele frequency. These genes were found to be highly concentrated in regions associated with nervous system function, including synaptic membranes, ion channels, and nicotinic acetylcholine receptors (nAChRs) — the primary targets of commercial pesticides. This finding strongly suggests that the widespread use of pesticides over the past century has likely become the main evolutionary driver of genomic change in A. cerana. This implies that the honeybee is undergoing a "genetic evolutionary race" to adapt to the chemical environment created by humans.
The "Time Capsule" from Malaysia
Further analyses revealed that the modern Malaysian honeybee population retained more "ancient" genetic characteristics in these rapidly evolving gene regions. This makes them a potential "historical archetype" of A. cerana, suggesting they may exhibit weaker resistance to pesticides. A clothianidin exposure experiment showed that honeybees from Central China had a significantly higher survival rate after 14 days of exposure compared to the Malaysian population. The Malaysian bees exhibited high mortality even at low pesticide concentrations. Transcriptome analysis further revealed that the X3 transcript of the nAChR α gene was significantly downregulated in the Central China population. This transcriptional change is likely closely linked to their enhanced pesticide resistance.
This study establishes a novel framework for quantifying population declines and provides policymakers with scientifically-guided strategies to monitor biodiversity changes, highlighting the irreplaceable value of museum specimens in evidence-based conservation. The phenotypic prediction and validation of the Malaysian population, which retains ancestral traits (functioning as a contemporary analogue of historical populations), provides an exemplar case applicable to numerous non-model species of conservation concern. Discovery of such populations fills a critical “missing-link” previously absent in most paleogenetic research, and thus enables the elucidation of mechanisms by which focal species deal with diverse environmental pressures. Lastly, this study also demonstrates how international specimen exchanges can overcome regional biodiversity documentation gaps in the post-globalization era with geo-political tensions.
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This study was supported by fundings from Ministry of Science and Technology of the People’s Republic of China, National Natural Science Foundation of China, Institute of Zoology, Chinese Academy of Sciences, Danish National Research Foundation.