Butterfly Resurrection: How Xerces Blue’s Genomic Legacy Is Shaping the Future of Insect Conservation

Summary

Analysis of the Xerces Blue butterfly genome unveils how prolonged population decline correlated with climate shifts led to its human-induced extinction. This study emphasizes the vulnerability of insects to climate fluctuations and highlights the crucial role of ancient genomic analysis in developing effective conservation strategies for threatened insect species.

News and Views by: Ella Wuichet (elwuichet@davidson.edu)
Primary Article: De-Dios et al. 2023

Disclaimer: This web page was produced as an assignment for an undergraduate course at Davidson College

Picture of the top and bottom of a Xerces Blue Butterfly (Glaucopsyche xerces). On the left, the butterfly is positioned so that the top side is showing. The wings have a blue-to-purple gradient color, and the body is fuzzy and black. On the right, the butterfly is positioned so its bottom side is showing. It appears mostly brown, with white spots throughout. Retrieved from Florida Museum 

Analysis of the Xerces Blue butterfly genome unveils how prolonged population decline correlated with climate shifts led to its human-induced extinction. This study emphasizes the vulnerability of insects to climate fluctuations and highlights the crucial role of ancient genomic analysis in developing effective conservation strategies for threatened insect species.

The Xerces Blue butterfly (Glaucopsyche xerces), characterized by its iridescent blue wings and distinctive white spots, inhabited the coastal sand dunes of San Fransisco from its discovery in 1852 until its extinction in 1941 (Grewe et al. 2021). Xerces Blue butterflies were a small population with an equally small range, and their larvae exclusively ate a native plant of their ecosystem called the common Deerwood (Acmispon glaber). As San Francisco continued to develop in the 1900s, the landscape began to change, and characteristic sandy soils were disrupted, leading to a sharp decline in common Deerwood plants and, as a result, a decline in the Xerces Blue butterflies that eventually led to their extinction (De-Dios et al. 2023). For years, scientists have been unable to study the extinct butterfly, but thanks to recent breakthroughs in genomic sequencing, scientists can now sequence ancient DNA samples from long-dead specimens. In this study, scientists sought to use ancient DNA from Xerces Blue butterflies to uncover their genetic information and demographic history, particularly focusing on understanding the factors that contributed to their extinction. 

Despite advances in modern sequencing technology, ancient DNA can be challenging to work with as it degrades into small fragments over time. While these fragments are still invaluable, assembling a complete genome using ancient DNA can be difficult as it is hard to position the small fragments in the correct order. To address this challenge, scientists studied the genetic relationship between Xerces Blue and its closest relative, the Silvery Blue butterfly (Glaucopsyche lygdamus), using the Silvery Blue genome to fill in the gaps in the Xerces Blue genome. To compare the genomes of these two species, the scientists used a known Palearctic Green-Underside Blue butterfly (Glaucopsyche alexis) genome with annotated gene functions. By combining the Xerces and Silvery Blue DNA samples and comparing them to a known butterfly genome, scientists were able to generate a complete genome for both species.

With complete genome sequencing information, the scientists began deciphering the ancestral relationships between the Xerces and Silvery Blue populations. They first used the information to confirm that the two species were indeed distinct and separate. They then created a phylogenetic tree, which is simply a graphical way to represent the ancestral relationships between species, and conducted a dated analysis to discover when the two species diverged. The analysis showed that the divergence of the Xerces and Silvery Blue populations occurred roughly 900,000 years ago. To trace more historical population dynamics of both butterflies, the scientists used an algorithm called the Pairwise Sequentially Markovian Coalescent. This algorithm showed that around 210,000 years ago, during the interglacial Marine Isotopic Stage 7, both populations saw an increase in effective population size, but after that, the trends differed (Desprat et al. 2006). This suggested that the populations adapted differently and inspired questions about genetic diversity. To study genetic diversity, they analyzed the number of individuals who possessed two different alleles for a particular gene (called heterozygosity). Individuals with high levels of heterozygosity were considered more genetically diverse because they had a larger selection of traits to express or pass to their offspring. Scientists found that Xerces Blue had 22% less heterozygosity than Silvery blue samples. Similarly, they saw that Xerces Blue individuals had large runs of homozygosity (RoH), meaning they had significant sections of their genome with the same allele for a particular gene. This was especially interesting as RoH often indicates inbreeding in small populations and would explain the Xerces Blue populations’ lack of genetic diversity.

Through this extensive analysis of the Xerces Blue genomic information, scientists could conclude that these butterflies experienced a severe demographic decline over their long history and that these declines were likely associated with climate change. Xerces Blue populations were already floundering, and human-mediated habitat destruction was the final blow in their extinction. These analyses also confirmed that Xerces Blue had low genetic diversity and high RoH, traits which made the population more vulnerable to environmental changes. 

Applying this newfound knowledge regarding Xerces Blues’ susceptibility to extinction due to small population sizes and low genetic diversity can help scientists identify similar patterns in other insects. Insects have comparatively larger population sizes than most vertebrates, which allows threatened insects to fly under the radar due to preconceived notions about extinction signals in vertebrates based solely on population size. This study emphasizes that extinction signals can look different in insects and may resemble the trends we saw in Xerces Blue. Using these new signals, we can more accurately measure how vulnerable insect populations react to climate change and help other species avoid extinction. 

Although this paper answers many vital questions, further research is still needed. One such avenue involves researching the differences between genomic extinction signals in vertebrates and insects, which may help solidify best conservation practices. Similarly, the transfer of genetic information from one species to another, also known as introgression, between the Xerces and Silvery Blue is still poorly understood, and further research may help clarify the last of the gaps in the two genomes. This paper also introduces some important ethical concerns. The complete Xerces Blue genome created by this study raises the potential for de-extinction practices involving gene editing to recreate a previously extinct organism (Seddon et al. 2014). De-extension is a hotly debated topic in the scientific community right now, and there are plenty of arguments for and against it, but the fact remains that improved sequencing of ancient DNA, like the work done in this study, makes de-extension a genuine possibility. 

References 

1. Grewe F, Kronforst MR, Pierce NE, Moreau CS. Museum genomics reveals the Xerces blue butterfly (Glaucopsyche xerces) was a distinct species driven to extinction. Biol Lett. 2021; 17(7): 20210123. [DOI: http://doi.org/10.1098/rsbl.2021.0123]
2. De-Dios T, Fontsere C, Renom P, Stiller J, Llovera L, Uliano-Silva M, Sánchez-Gracia A, Wright C, Lizano E, Caballero B, Navarro A, Civit S, Robbins RK., Blaxter M, Marquès-Bonet T, Vila R, Lalueza-Fox C. Whole-genomes from the extinct Xerces Blue butterfly can help identify declining insect species. eLife 2023; 12:RP87928 [DOI https://doi.org/10.7554/eLife.87928.2]
3. Desprat, S., Sánchez Goñi, M. F., Turon, J., Duprat, J., Malaizé, B., & Peypouquet, J. Climatic variability of Marine Isotope Stage 7: Direct land–sea–ice correlation from a multiproxy analysis of a north-western Iberian margin deep-sea core. Quaternary Science Reviews 2006; 25(9-10): 1010-1026. [DOI https://doi.org/10.1016/j.quascirev.2006.01.001]
4. Seddon PJ, Moehrenschlager A, Ewen J. Reintroducing resurrected species: selecting DeExtinction candidates. Trends Ecol Evol. 2014; 29(3):140-7. [DOI: https://doi.org/10.1016/j.tree.2014.01.007]

© Copyright 2024 Department of Biology, Davidson College, Davidson, NC 28036