Historical and modern genomes for quantifying temporal genomic erosion in a nationally endangered butterfly

PopGroup59, Lille, France, Jan 2026

Rebecca Whitla, James Hogan, Geoff Martin, Tim Shreeve, Saad Arif*

*Dept. of Biological and Medical Sciences, Oxford Brookes University

Motivation for quantifying genomic erosion

  • Identifying genetic threats to small populations

  • Is it possible to identify at-risk populations/species using genomic data alone?

  • Pitfalls of using genomic data from only modern samples/Weak correlation between contemporary gentic diversity and extinction risk (IUCN assessments) (Diez-del-Molino et al., 2018; Teixeira & Huber, 2021)

  • Potential of using temporal assessments (in particular the use of museum specimens) of genomic erosion for conservation monitoring and management:

Figure from: Diez-del-Molino et al., 2018. Trends in Ecology & Evolution 33(4): 282-292.

The wide-spread Leptidea sinapis L. (wood white) is endangered in Great Britain


  • Widely distributed across Europe and central Asia

  • Species of Least Concern (IUCN) in EU

  • Considered endangered in Great Britain due to distributional trends (Fox et al., 2022) and previous assessment (2010)

Demographic decline in the 1980s followed by stablilization

  • Systematic monitoring by the UK Butterfly Monitoring Scheme (UKBMS) since 1976

  • Relative abdundance data (averaged across sites) show a sharp decline c. 1985 but demographic stability since then.

Image: https://ukbms.org/species/wood-white

However, distributional decline continues..

  • Distributional decline continued beyond this time was -71% from 2005-2015 but decreasing to ~33% between 2010-2019(Fox et al., 2022)

  • Potential downgrading of threat status from endangered to vulnerable in GB in upcoming assessments

Data: GBIF.org (7 October 2025) https://doi.org/10.15468/dl.ffudep

Aim: Evaluating temporal genomic erosion in British L. sinapis


  • Provide a baseline assessment of genomic erosion in a nationally threatened butterfly species

  • Compare metrics of genomic erosion between historical (1913-1971) and modern (2022) samples:

    • Does turonver in genomic erosion reflect demographic trends?
    • Which metrics of genomic erosion is most useful?

  • Could future recovery and resilience be hindered by loss of genetic diversity and accumulation of genetic load?

  • Inform conservation management strategies?

Temporal and Spatial sampling

  • Historical GB samples (1913-1971): DEVH = 9, NTHH = 6
  • Modern GB samples (2022): DEV = 5, NTH = 5
  • Modern Eurasian samples (2013-2015, from Talla et al, 2017, GBE): SWE=10, SPA=10, KAZ=10
  • WGS at 4-20X depth of coverage

Decreasing connectivity between GB populations

  • SPA was far to distinct from all POPs, hence not included in this PCA
  • Fst nearly doubles between historical and modern GB populations (0.066 to 0.12)
  • NTH populations remain largely unchanged

No consistent signal of genomic erosion in genome-wide heterozygosity

  • NTH shows most marked decrease in heterozygosity

  • impact of depth of coverage?

Runs-of-Homozygosity (RoH) suggest bottlenecks in the 20th Century

  • RoH inferred using RoHan(left; Renaud et al., 2019) and
  • Evidence for potential bottleneck in DEV ~25 generations. Earlier bottlneck in NTH ~50 generations (back-of-envelope calculations; van der Valk et al., 2019; Thompson, 2013) (right)

Estimating contemporary Ne using LD from modern samples

  • LD-based estimates of recent Ne using GONe (Santiago et al., 2020) also suggest receent contraction in DEV versus NTH
  • Results surprisingly consistent with RoH-based results (previous slide)
  • Results highly dependent on pedigree of individuals but perhaps improves for smaller populations (bootstrapping of SWE individuals)?

Little evidence for overwhelming drift increasing genetic load

  • General trends of decrease in allele frequencies of high (e.g. loss-of-function) and moderate (e.g. missense) impact variants over time within GB populations.
  • Signal of purifying selection for high impact variants in DEV
  • Caveats:
    • Sample size (n=3-6 for GB pops) limitations may affect power to detect subtle changes in genetic load over time.
    • Realized load for moderate impact variants shows increase over time particularly in NTH

Summary

  • Decreasing connectivity between L. sinapis GB populations over the last 100 years

  • Changes in distributions of RoH show consistent/expected signals of decline associated with declines in dsitribution.

  • Conservation implications: Accumulation of strongly deleterious not strongly supported over this time period, however increase in moderately/weakly deleterious variants and continual loss of genetic diversity may incur fitness costs and limit future adaptive potential

  • Pre-decline/museum samples help clarify recent changes in populations size even with small sample sizes (would be useful for taxa difficult to monitor by other means)

  • Sequencing of museum samples to a similar effort as modern samples still remains pricey due to larger sequencing lengths of recent hight-throughput sequencing platforms.

  • Any suggestions/criciticism/discussion welcome!

Acknowledgements

Rebecca Whitla (PhD student)

Collaborators:

Prof Tim Shreeve

Geoff Martin (NHM, London)

Dr. James Hogan (OUMNH, Oxford)

Other:

Natural England for license to collect modern L. sinapis samples. Jack Medlock and Forestry England for permission to collect samples in Northamptonshire. Ian Chadwick and Devon Wildlife Trust for permission to collect samples in Devon.

Darwin Tree of Life for high-quality L. sinapis reference genome and annotation


Funding:

Nigel Groome Studentship to RW by Dept. of BMS, Oxford Brookes University


More Info:

https://saadarif.github.io

sarif@brookes.ac.uk

Join the LepEU Consortium!

https://lepeu.github.io

Heterozygoisty over time

FRoH over time

Using RZooRoH (Druet & Gautier, 2017)