Xerces Blue butterflies were once frequent visitors to dunes along the coastline of San Francisco. They disappeared at the beginning of the 1940s. Image source Science Source / The Natural History Museum, London

The final one of Xerces Blues died in the 1940s; the species was the first butterfly known to have been threatened due to urbanization throughout North America. Around three years ago, an international group of geneticists began studying DNA sequences from Xerces Blue specimens–long stored in museums to seek genetic clues that could explain the journey to its eventual disappearance. The results published recently in eLife, reveal that the species’ population was shrinking for tens of thousands of years, suggesting that this butterfly had been highly vulnerable at the time it had to contend with human-driven habitat loss. The situation of Xerces Blue could shed some light on the evolution of other bugs.

These lavender-colored wings of the Xerces Blue butterfly (Glaucopsyche xerces) were often seen over sand dunes on San Francisco’s coastline; the species has its only home. With the advent of roads and housing replacing dunes and dunes, the Xerces Blue saw fewer plants that could sustain its larvae and then ended up dying out. In the meantime, the closely similar Silvery Blue butterfly (G. Lygdamus) that thrives over an even larger area, from Alaska to Baja California, lived.

To investigate the evolutionary background of extinct Xerces Blue and to compare it with its widespread cousin, The team consulted specimens of both species found within the Smithsonian National Museum of Natural History in Washington, DC. A tiny portion of an abdomen was carefully taken from five Xerces Blue butterflies collected between 80 and 100 years ago and from a recently taken Silvery Blue specimen, together with seven other older, more ancient Silvery Blue specimens.

Researchers then extracted DNA from these small segments and sequenced them to determine the DNA for each sample. The majority, excluding one Xerces Blue sample, contained usable DNA. “As far as I know, these are the first complete genomes of an extinct insect,” claims the study’s lead, author Carles Lalueza Fox, an evolutionary biologist who is also the director at the Museum of Natural Sciences of Barcelona in Spain.

The team utilized these genomes to construct the phylogenetic tree. This will determine how closely the two specimens are related based on similarity to gene expression patterns. The branching pattern in this tree suggests that the butterflies separated into distinct types about 900,000 years ago.

The researchers then employed an algorithm to calculate changes in the population size over time based on genetic diversity in the genomes of each specimen. If the insect’s paternal and maternal chromosomes match in a variety of places, the absence of diversity could indicate that the species is prone to breeding due to the tiny populations.

The results across all the specimens suggest that Xerces Blue’s population progressively decreased during the last glacial period, beginning about 75,000 years ago; however, the Silvery Blue’s population increased, despite changes in the climate.

These Xerces Blue genomic samples contained evidence of low genetic diversity,, often resulting from shrinking populations. For instance, Xerces Blue samples had longer chromosomes, which included identical genes from every parent. Additionally, they had more harmful mutations, which could be removed from the population by natural selection if the population size had been greater. Thus, when San Francisco’s growing footprint stripped the butterfly of its natural habitat, this fragile species could not adjust.

Researchers had previously wondered if Xerces Blue and Silvery Blue butterflies were sim,ilar species. The current study confirms the work done by evolutionary biologist and entomologist Corrie Moreau from Cornell University and colleagues, who in 2021 identified Xerces Blue as a distinct species by using DNA from a single specimen in the museum.

The latest eLife paper outlines “potential measures of a species on its way to extinction,” says Moreau, who was not a part of the study. By analyzing the genomes of various Xerces Blue specimens, the researchers “capture the genomic signatures of a species on its way to collapse,” she says.

The identical signatures of genomics, namely, low genetic diversity and the accumulation of mutations, could be used to pinpoint current insects whose populations are at risk, even when researchers have access only to a single person from the species, according to Lalueza-Fox. “Imagine you spot a brand new species of beetle the jungle, you study it and see the similar patterns. It is possible to suspect that the species could be endangered or being extinct.”