Whole-genomes from the extinct Xerces Blue butterfly reveal low
diversity and long-term population decline
Toni de-Dios1+, Claudia Fontsere1+,
Pere Renom1+, Josefin Stiller2, Laia
Llovera1, Marcela Uliano-Silva3,
Charlotte Wright3, Esther Lizano1,4,
Arcadi Navarro1,5, Robert K.
Robbins6, Mark Blaxter3, Tomàs
Marquès-Bonet1,4,5,7*, Roger Vila1*,
Carles Lalueza-Fox1*
1Institute of Evolutionary Biology (CSIC-Universitat
Pompeu Fabra), 08003 Barcelona, Spain
2Centre for Biodiversity Genomics, University of
Copenhagen, DK-2100, Denmark
3Wellcome Sanger Institute, Hinxton, Saffron Walden
CB10 1RQ, UK
4Institut Català de Paleontologia Miquel Crusafont,
Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès,
Barcelona, Spain
5 Catalan Institution of Research and Advanced Studies
(ICREA), 08010 Barcelona, Spain
6 Department of Entomology, National Museum of Natural
History, Smithsonian Institution, Washington, DC 20013-7012, USA
7 CNAG-CRG, Centre for Genomic Regulation, Barcelona
Institute of Science and Technology (BIST), 08036 Barcelona, Spain
+ equally contributed
*Corresponding Authors
Carles Lalueza-Fox
Tomas Marquès-Bonet
Roger Vila
Email: carles.lalueza.fox@gmail.com
Abstract
The Xerces Blue (Glaucopsyche xerces ) is considered to be the
first butterfly to become extinct at global scale in historical times.
It was notable for its chalky lavender wings with conspicuous white
spots on the ventral wings. The last individuals were collected in their
restricted habitat, in the dunes near the Presidio military base in San
Francisco, in 1941. To explore the demographic history of this iconic
butterfly and to better understand why it went extinct, we sequenced at
medium coverage the genomes of four 80 to 100-year-old Xerces Blue
specimens and seven historic specimens of its closest relative, the
Silvery Blue (G. lygdamus ). We compared these to a novel
annotated genome of the Green-Underside Blue (G. alexis ).
Phylogenetic relationships inferred from complete mitochondrial genomes
indicate that Xerces Blue was a distinct species that diverged from the
Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes,
we show that both species experienced population growth during the MIS 7
interglacial period, but the Xerces Blue decreased to a very low
effective population size subsequently, a trend opposite to that
observed in the Silvery Blue. Runs of homozygosity in the Xerces Blue
were significantly greater than in the Silvery Blue, suggesting a higher
incidence of inbreeding. In addition, the Xerces Blue carried a higher
proportion of derived, putatively deleterious amino acid-changing
alleles than the Silvery Blue. These results demonstrate that the Xerces
Blue experienced more than 100 thousand years of population decline,
prior to its human-induced final extinction.
Keywords: Extinction, Ancient Genomics, Butterflies, Population
Genomics, Xerces Blue