Autozygosity and genetic load as sensitive early warnings of butterfly population decline
- 1Marche Polytechnic University Ancona - University School for Advanced Studies Pavia
Abstract
Insects are commonly expected to be protected from genomic erosion by high fecundity, short generation times, and large census sizes. Yet, insect populations can decline and eventually go extinct, underscoring the need for genomic indicators that provide actionable early warnings of population collapse. Here, we test this expectation by comparing contemporary and historical genomes of the Ponza grayling, Hipparchia sbordonii, an endangered butterfly endemic to the Pontine Islands in the Mediterranean, with the genomes of a widespread European congeneric species, H. semele. Using whole-genome resequencing, outgroup-based variant polarization, demographic reconstruction, runs of homozygosity, selection scans, and annotation-based genetic-load analyses, we show that H. sbordonii has undergone sustained demographic contraction, including a sharp recent decline. Despite limited temporal change in mean genome-wide heterozygosity, we observe extensive autozygosity, elevated inbreeding, and a clear shift from masked to realized genetic load in contemporary H. sbordonii. R'XY analysis revealed similar relative frequencies of high-impact derived variants in H. sbordonii and H. semele, suggesting ineffective purging during population collapse, whereas low- and moderate-impact variants were relatively enriched in H. sbordonii, particularly within candidate regions under selection. This indicates a more complex dynamic, in which functional variation has been shaped by the combined effects of drift, relaxed purifying selection, and possible local adaptation. Our study shows that declining butterfly populations bear distinctive signatures of genomic erosion, mirroring patterns well documented in vertebrates. Yet recent demographic collapse in H. sbordonii is more clearly captured by long runs of homozygosity and realized genetic load than by changes in mean genome-wide heterozygosity, highlighting their potential as early warning indicators for monitoring declining insect populations.
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BibTeX
@misc{fava2026autozygosity,
title = {{Autozygosity and genetic load as sensitive early warnings of butterfly population decline}},
author = {S. Fava and M. Gargano and D. Kireta and P. Gratton and D. Cesaroni and A. Iannucci and C. Ciofi and R. Biello and M. Gerdol and G. Bertorelle and E. Trucchi},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.05.742957},
url = {https://www.biorxiv.org/content/10.64898/2026.08.05.742957v2},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Autozygosity and genetic load as sensitive early warnings of butterfly population decline
AU - S. Fava
AU - M. Gargano
AU - D. Kireta
AU - P. Gratton
AU - D. Cesaroni
AU - A. Iannucci
AU - C. Ciofi
AU - R. Biello
AU - M. Gerdol
AU - G. Bertorelle
AU - E. Trucchi
PY - 2026
DA - 2026/08/05
PB - bioRxiv
DO - 10.64898/2026.08.05.742957
UR - https://www.biorxiv.org/content/10.64898/2026.08.05.742957v2
AB - Insects are commonly expected to be protected from genomic erosion by high fecundity, short generation times, and large census sizes. Yet, insect populations can decline and eventually go extinct, underscoring the need for genomic indicators that provide actionable early warnings of population collapse. Here, we test this expectation by comparing contemporary and historical genomes of the Ponza grayling, Hipparchia sbordonii, an endangered butterfly endemic to the Pontine Islands in the Mediterranean, with the genomes of a widespread European congeneric species, H. semele. Using whole-genome resequencing, outgroup-based variant polarization, demographic reconstruction, runs of homozygosity, selection scans, and annotation-based genetic-load analyses, we show that H. sbordonii has undergone sustained demographic contraction, including a sharp recent decline. Despite limited temporal change in mean genome-wide heterozygosity, we observe extensive autozygosity, elevated inbreeding, and a clear shift from masked to realized genetic load in contemporary H. sbordonii. R'XY analysis revealed similar relative frequencies of high-impact derived variants in H. sbordonii and H. semele, suggesting ineffective purging during population collapse, whereas low- and moderate-impact variants were relatively enriched in H. sbordonii, particularly within candidate regions under selection. This indicates a more complex dynamic, in which functional variation has been shaped by the combined effects of drift, relaxed purifying selection, and possible local adaptation. Our study shows that declining butterfly populations bear distinctive signatures of genomic erosion, mirroring patterns well documented in vertebrates. Yet recent demographic collapse in H. sbordonii is more clearly captured by long runs of homozygosity and realized genetic load than by changes in mean genome-wide heterozygosity, highlighting their potential as early warning indicators for monitoring declining insect populations.
ER -