When COI barcodes deceive: complete genomes reveal introgression in hairstreaks.
Two species of hairstreak butterflies from the genusCalycopisare known in the United States:C. cecropsandC. isobeonAnalysis of mitochondrial COI barcodes ofCalycopisrevealedcecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central AmericanCalycopisspecies. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27Calycopisspecimens of four species:C. cecrops,C. isobeon,C. quintanaandC. bactraSome of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USACalycopiswith atypical barcodes grouped with Central American speciesC. quintanaby mitochondria, nuclear genome trees placed them within typical USAC. cecropsin agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially betweenC. cecropsandC. isobeonAbout 2.3% of eachC. cecropsgenome has probably (p-value < 0.01, FDR < 0.1) introgressed fromC. isobeonand about 3.4% of eachC. isobeongenome may have come fromC. cecrops.The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.
Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA.
Qian
0000-0002-8909-0414
Q
Cong
Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA.
Jinhui
J
Shen
Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA.
Dominika
D
Borek
Department of Entomology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, NHB Stop 105, Washington, DC, USA.
Robert K
RK
Robbins
Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA.
Paul A
PA
Opler
Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA.
Zbyszek
Z
Otwinowski
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA grishin@chop.swmed.edu.|Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA.
Nick V
NV
Grishin
D000818:Animals; D002080:Butterflies / Q000254:growth & development*; D002489:Central America; D058893:DNA Barcoding, Taxonomic; D004272:DNA, Mitochondrial / Q000235:genetics; D049750:Genome, Insect; D054629:Genome, Mitochondrial; D010802:Phylogeny; D014481:United States
D004272:DNA, Mitochondrial
Lepidoptera; blues and hairstreaks; comparative genomics; phylogeny; speciation; taxonomy