Speciation in cloudless sulphurs gleaned from complete genomes

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 tostudy speciationmechanisms andthelinkbetweengenotype andphenotypeusing completegenomes.We sequenced and assembled a complete genomeof theCloudless Sulphur (Phoebis sennae) from a single wild-caught specimen. This genome was used as reference to compare genomes of six specimens, three fromthe eastern populations (Oklahoma and north Texas), referred to as a subspecies Phoebis sennae eubule, and three fromthe southwestern populations (south Texas) known as a subspecies Phoebis sennae marcellina.While the two subspecies differ only subtly in phenotype andmitochondrial DNA, comparison of their complete genomes revealed consistent and significant differences,which aremore prominent than those between tiger swallowtails Pterourus canadensis and Pterourus 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 flowmainly from P. s. marcellina to P. 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.