title: Speciation in Cloudless Sulphurs Gleaned from Complete Genomes.
abstract: For 200 years, zoologists have relied on phenotypes to learn about the evolution of animals. A glance at the genotype, even through several gene markers, revolutionized our understanding of animal phylogeny. Recent advances in sequencing techniques allow researchers to study speciation mechanisms and the link between genotype and phenotype using complete genomes. We sequenced and assembled a complete genome of the Cloudless Sulphur (Phoebis sennae) from a single wild-caught specimen. This genome was used as reference to compare genomes of six specimens, three from the eastern populations (Oklahoma and north Texas), referred to as a subspeciesPhoebis sennae eubule, and three from the southwestern populations (south Texas) known as a subspeciesPhoebis sennae marcellina While the two subspecies differ only subtly in phenotype and mitochondrial DNA, comparison of their complete genomes revealed consistent and significant differences, which are more prominent than those between tiger swallowtailsPterourus canadensisandPterourus glaucus The two sulphur taxa differed in histone methylation regulators, chromatin-associated proteins, circadian clock, and early development proteins. Despite being well separated on the whole-genome level, the two taxa show introgression, with gene flow mainly fromP. s. marcellinatoP. s. eubule Functional analysis of introgressed genes reveals enrichment in transmembrane transporters. Many transporters are responsible for nutrient uptake, and their introgression may be of selective advantage for caterpillars to feed on more diverse food resources. Phylogenetically, complete genomes place family Pieridae away from Papilionidae, which is consistent with previous analyses based on several gene markers.
authors.affiliation: Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center.
authors.forename: Qian
authors.initials: Q
authors.lastname: Cong
authors.affiliation: Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center.
authors.forename: Jinhui
authors.initials: J
authors.lastname: Shen
authors.affiliation: McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Warren
authors.affiliation: Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center.
authors.forename: Dominika
authors.initials: D
authors.lastname: Borek
authors.affiliation: Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center.
authors.forename: Zbyszek
authors.initials: Z
authors.lastname: Otwinowski
authors.affiliation: Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center Howard Hughes Medical Institute, University of Texas Southwestern Medical Center grishin@chop.swmed.edu.
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D000818:Animals; D002965:Classification; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D051456:Gene Flow; D049750:Genome, Insect; D054629:Genome, Mitochondrial / Q000235:genetics; D005838:Genotype; D007915:Lepidoptera / Q000145:classification / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: Phoebis sennae; comparative genomics; introgression; lepidoptera; phylogeny; speciation