Aporia crataegi (the black-veined white) extirpated in Great Britain ~1925

“frequently able to capture five or six specimens at one stroke of the net” - Goss, 1887

Also extirpated in the Netherlands and Korea

Images: Todisco et al 2020, Sci. Rep.

The spasmodic decline of A. crataegi in Britain?





  • Exhibit a ‘spasmodic’, rather than gradual decline, eastwards throughout the 19th Century (Dennis, 1977)

  • Anecdotal recordings of multiple releases of European stock (Pratt, 1983)

Images: Dennis, RLH, 1977 The British Butterflies

Potential reasons behind the demise of A. crataegi in Britain


  • Debate on reasons of extinction (Pratt, 1983):

    • Avian predation (increase in small birds)
    • fungal, viral or other pathogen
    • Series of unseasonably wet Septembers around years of low A. crataegi abundance in the 19th Century


  • Likely, a combination factors led to its demise, possibly a combination of wet conditions + fungal infection

A genomic perspective on the demise of A. crataegi in Britain


Goals:

  1. How did the effective population size of the A. crataegi change around and after the colonization of Britain?

  2. Is there further evidence of population size reduction in the 19th century due to inbreeding in a declining population?

  3. Are there any signs of decline in individual genetic fitness?

  4. Is there any evidence for a role of pathogen infection in the extirpation of UK butterflies?

A complementary analysis on Polyommatus icarus common blue, using modern specimens, as an example of a demographically stable species, in recent times, but with a similar post-glacial colonisation history.

Methods: Field work & library prep



  • Sampled specimens only where collection year and locality was available

  • 1-2 legs per butterfly dissected for DNA extraction/library prep

  • Based on pilot work, we got more endogenous read data from leg-template sequencing libraries rather than abdomens

  • Library prep kit (NEB Ultra II DS DNA) led to partial repair on 5’ ends

  • Further details can be found in Whitla et al. 2024, Mol Ecol

Results: Data Quality and Yield


  • A. crataegi samples ranged from 1854-1924

  • Average depth ranged from 2-13X:

    • European: 10X (n=4), GB 6X (n=13). Two GB samples had average depth <5X

  • Average coverage ≥50% at depth of ≥5X

  • Historical damage profile:

  • P. icarus samples collected in 2017-2018. Depth 11-50X
    • European: n=3, GB n=4

Whitla et al. 2024, Mol Ecol

Results: British A. crataegi are distinct from European

  • PCA based on genotype likelihoods
  • Isolation by distance pattern within GB
  • Evidence of European stock releases in late 19th/early 20th century or potential mislabeling. Labelled as European for downstream analysis
  • Youngest specimen (Herne bay, Kent, 1924) clusters with European specimens

Whitla et al. 2024, Mol Ecol

Results: Evidence of bottleneck at time of post-glacial colonisation

Whitla et al. 2024, Mol Ecol

Results: Inbreeding suggest more recent population declines GB A. crataegi

  • Runs of Homozygosity (RoHS) of ≥ 1 megabase (Mb) cover 1.6% of the A. crataegi genome compared to 0.1% and none in P. icarus

Whitla et al. 2024, Mol Ecol

Results: No increase in total genetic load

  • But there was an increase in homozygous missense (ns)and synonymous(*) variants in GB A. crataegi
  • Caveat: Variant effects predicted by snpEFF based on Ensembl annotation

Whitla et al. 2024, Mol Ecol

Results: Potential increase in genetic load in shared derived alleles

  • An Rxy >1 implies a relative increase in frequency in GB compared to EU, whereas <1 implies a relative decrease

  • Caveat: low to very low sample sizes for allele frequency estimations

Whitla et al. 2024, Mol Ecol

Conclusions


  • A. crataegi underwent severe bottlneck at time of post-glacial colonisation and never seems to have recovered.

  • Increases in homozygosity (RoH ≥ 1 Mb) consistent with a ‘spasmodic’ rather than gradual decline

  • Increase in homozygous missense mutations and shared derived alleles may have made population more prone to extinction


  • Consistent differences in genomic erosion suggest these metrics could be helpful to monitor or identify threatened insect populations/species with a small number of individuals (e.g. 4-6 ;see also de Dios et al., 2023, Nolen et al., 2024)

  • Our DNA extraction + Library prep works well for museum specimens:

    • use of legs keeps curators mostly happy

    • ≥50% coverage at depth of ≥5X for ~175 yo specimens, ≥90% coverage at depth of ≥5X for ~120 yo specimens

    • further room for optimization

Ongoing work: Did fungal (or other) pathogens contribute to the regional extinction?



  • Metagenomic profiling using aMeta
    (https://github.com/NBISweden/aMeta)

  • Many issues:

    • sample size (specific)
    • distinguishing peri- and postmortem degradation
    • Unclear how much temporal resolution damage on historical DNA can offer
    • high potential!

Unpublished data

Acknowledgements

Rebecca Whitla (PhD student)

Collaborators:

Prof Tim Shreeve

Dr. Casper Breuker

Dr. Korneel Hens

Geoff Martin (NHM, London)

Dr. James Hogan (OUMNH, Oxford)

Other:

Kornad Lohse and Darwin Tree of Life


Funding:

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


More Info:

https://saadarif.github.io

sarif@brookes.ac.uk

the ‘scrolltelling’ experience: https://saadarif.github.io/BVW-LastDays