Chromosomes as Barcodes: Discovery of a New Species of Black Fly (Diptera: Simuliidae) from California, USA.

Abstract

Simple SummaryThe discovery and elucidation of species, especially those that are structurally similar, often require special tools and approaches. The basic principle of a unique barcode, as used in retail stores and more recently as DNA sequences in taxonomy, is also inherent in the giant banded chromosomes of flies (Diptera). We used the sequence of chromosome bands—the barcode—in the discovery of a new species of black fly from California, USA. The chromosomal barcode indicates this species is unique among all others in the Simulium (Boreosimulium) annulus group to which it belongs. To provide an integrated taxonomic approach, we analyzed and described the larvae, pupae, males, and females of this new species and assigned the formal name Simulium ustulatum n. sp. We also provided a traditional DNA barcode using the cytochrome c oxidase I (COI) gene. The new species has the most rearranged chromosomes of all North American members of its species group and differs most conspicuously by having a large chromocenter from which all six chromosome arms radiate. The species is structurally unique in the larva and male. The COI barcode enables identification of the female and pupa, which are structurally similar to other species in the group. The new species is the only western North American member of the Simulium annulus group that inhabits low-elevation, disturbed landscapes.One of the most popular tools for species discovery and resolution is the DNA barcode, typically based on the cytochrome c oxidase I (COI) gene. However, other non-genic barcodes are available for Diptera. The banding sequence of polytene chromosomes in some dipteran cells, particularly of the larval silk glands, can provide a unique species barcode. We used the sequence of bands to reveal a new species of black fly in the Simulium (Boreosimulium) annulus species group from California, USA. To further characterize the species and provide more integrated taxonomy, we morphologically described all life stages above the egg, formally named the species Simulium ustulatum n. sp., and provided a conventional COI barcode. The COI barcode confirmed the chromosomal and morphological evidence that the species is a new member of the S. annulus group, and enabled identification of the larva and female, which are structurally similar to those of other species. The chromosomal barcode shows that this species has the most rearranged complement, compared with the eight other North American members of its species group, with up to 12 times the number of fixed rearrangements. Up to six chromosomal rearrangements, including autosomal polymorphisms and sex-linked phenomena, are shared with other members of the group. The most unique and conspicuous chromosomal feature of this new species is a large, pale-staining chromocenter from which the six chromosomal arms radiate. The distribution of this univoltine species in lowland rivers of California’s Central Valley could make it vulnerable, given climate change and increasing land development.