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      When COI barcodes deceive: complete genomes reveal introgression in hairstreaks

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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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          Author and article information

          Journal
          Proc Biol Sci
          Proc. Biol. Sci
          RSPB
          royprsb
          Proceedings of the Royal Society B: Biological Sciences
          The Royal Society
          0962-8452
          1471-2954
          8 February 2017
          : 284
          : 1848
          : 20161735
          Affiliations
          [1 ] Howard Hughes Medical Institute, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
          [2 ] Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
          [3 ] Department of Entomology, National Museum of Natural History, Smithsonian Institution , PO Box 37012, NHB Stop 105, Washington, DC, USA
          [4 ] Department of Bioagricultural Sciences and Pest Management, Colorado State University , Fort Collins, CO 80523-1177, USA
          Author notes

          Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.3672202.

          Author information
          http://orcid.org/0000-0002-8909-0414
          Article
          PMC5310595 PMC5310595 5310595 rspb20161735
          10.1098/rspb.2016.1735
          5310595
          28179510
          a9a48efd-8a69-447d-8141-47343f0e1781
          © 2017 The Author(s)

          Published by the Royal Society. All rights reserved.

          History
          : 28 August 2016
          : 9 January 2017
          Funding
          Funded by: National Institute of General Medical Sciences, http://dx.doi.org/10.13039/100000057;
          Award ID: GM094575
          Funded by: Welch Foundation, http://dx.doi.org/10.13039/100000928;
          Award ID: I-1505
          Categories
          1001
          22
          70
          198
          Genetics and Genomics
          Research Article
          Custom metadata
          February 8, 2017

          taxonomy,Lepidoptera,blues and hairstreaks,speciation,comparative genomics,phylogeny

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