When coi barcodes deceive

Complete genomes reveal introgression in hairstreaks

Qian Cong, Jinhui Shen, Dominika Borek, Robert K. Robbins, Paul A. Opler, Zbyszek Otwinowski, Nick V. Grishin

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon. Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra. Some 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 USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon. About 2.3% of each C. cecrops genome has probably (p-value, 0.01, FDR,0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. 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.

Original languageEnglish (US)
Article number20161735
JournalProceedings of the Royal Society B: Biological Sciences
Volume284
Issue number1848
DOIs
StatePublished - Feb 8 2017

Fingerprint

barcoding
introgression
genome
Genes
Genome
nuclear genome
Bactra
mitochondria
Mitochondria
mitochondrion
Lycaenidae
transmembrane proteins
Butterflies
Museums
Lepidoptera
Mitochondrial Genome
mitochondrial DNA
Protein Transport
Gene encoding
protein

Keywords

  • Blues and hairstreaks
  • Comparative genomics
  • Lepidoptera
  • Phylogeny
  • Speciation
  • Taxonomy

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Environmental Science(all)
  • Agricultural and Biological Sciences(all)

Cite this

When coi barcodes deceive : Complete genomes reveal introgression in hairstreaks. / Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K.; Opler, Paul A.; Otwinowski, Zbyszek; Grishin, Nick V.

In: Proceedings of the Royal Society B: Biological Sciences, Vol. 284, No. 1848, 20161735, 08.02.2017.

Research output: Contribution to journalArticle

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abstract = "Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon. Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6{\%} different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra. Some 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 USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon. About 2.3{\%} of each C. cecrops genome has probably (p-value, 0.01, FDR,0.1) introgressed from C. isobeon and about 3.4{\%} of each C. isobeon genome may have come from C. 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.",
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