Discussion
We have used a modern reference genome and ancient DNA genome sequence
data from museum specimens to explore the relationships and historical
population genetic history of an extinct butterfly, the Xerces Blue.
Based upon a near-complete mtDNA genome from a Xerces Blue specimen,
Grewe et al. (2021) (3) proposed that the Xerces Blue and the Silvery
Blue were distinct species. We confirm this finding using full
mitochondrial genomes and extensive nuclear genomic data from multiple
specimens. Given the lack of evidence for Wolbachia infection, a
detailed analysis of genomic architectures could help identify barriers
to introgression between these species.
We provide evidence for low population size in Xerces Blue, correlated
with low genetic variation, a higher proportion of runs of homozygosity
and increased frequency of deleterious, amino acid-changing alleles
(14–16). However, there was no genetic evidence of recent inbreeding,
which sometimes occurs in critically endangered species (17,18). Our
analyses indicate that the Xerces Blue had experienced a severe
demographic decline for tens of thousands of years, likely associated
with changing climatic factors. Thus, the destruction of the Xerces Blue
habitat by humans was likely the final blow in the extinction process.
We suggest that endangered insects with demographic traits indicative of
long-term low effective population size should be considered to be
especially vulnerable to extinction.
The generation of these paleogenomes is the first step towards
understanding the specific adaptations of Xerces Blue butterfly. Maybe
the most conspicuous of these was a pattern of white spots, usually
without black ocelli, on their ventral wing surfaces. Genes such asWnt , optix and cortex are associated with
pigmentation wing patterns in butterflies (19–23). It may be
informative to identify amino acid differences in these and other genes
and to undertake functional studies, such as those based on CRIPSR-Cas 9
knock-outs, in extant relatives to elucidate relevant phenotypic and
genomic characteristics of this extinct butterfly. However, in our
preliminary screening in these pigmentation genes, no amino acid changes
as compared to the Silvery Blue genomes have been discovered, raising
the question if potential differences could be in fact in regulatory
regions. However, it is likely that this question would need to further
increase the coverage of the paleogenomes generated. Irrespective of
this, our study further demonstrates the value of ancient DNA in museum
specimens for evolutionary studies at a population scale.
In addition to, Glaucopsyche alexis is a good reference genome to
study the transition from mutualism with ants to parasitism on ants
within subtribe Glaucopsychina; the latter group includes the
remarkable Phengaris butterflies, which are ant-parasites in the
last instars and are currently endangered in Europe (mainly due to their
highly specialised strategy) (24). The G. alexis reference genome
(coupled with those of the Xerces Blue and Silvery Blue) will help to
understand the evolution from an exclusively herbivorous diet in later
instars to a aphytophagous one and the biochemical synthesis of
molecules used in the ant-parasitic relationship.