Callophrys elfins are a group of North American butterflies from the order Lepidoptera. Callophrys elfins are some of the earliest butterflies to emerge in the spring and several species frequently co-occur in isolated pine barren habitats. Despite a high risk of decline due to anthropogenic habitat disturbance and early spring warming, limited genomic resources are available for conducting population and conservation genetic studies in this group. This dissertation work describes a new reference genome for Callophrys niphon, the eastern pine elfin. PacBio HiFi sequencing was used to assemble the 556 Mb genome, comprising 22 autosomes and a Z (sex) chromosome. Gene annotation and mapping of conserved portions of ancestral lepidopteran chromosomes, known as Merian elements, revealed a putative chromosomal fusion. Merian elements 1, 9, and 19 formed the largest C. niphon chromosome. The reference genome was used to align short-read sequences from multiple additional species including individuals from C. augustinus, C. polios, C. irus, and C. henrici. New phylogenies were constructed for different regions of the genome. These genome-wide data were also used to investigate gene flow and hybridization among Callophrys elfins due to their high degree of range overlap. There was little evidence for current gene flow among species, but introgression has likely occurred after past hybridization among several species of Callophrys elfin, including C. polios, C. henrici and C. augustinus. C. niphon exhibits a longer flight period than other Callophrys species and the association of genetic variation with this phenological variation was explored by comparing early and late emerging individuals across multiple populations. Overall genetic differentiation was low in C. niphon populations between both early and late emerging individuals and geographically separate populations. However, a genome-wide association analysis revealed candidate genes possibly associated with emergence time. Population genetic analyses conducted across all populations of C. niphon suggested a history of a small population size (a genetic bottleneck) followed by a recent population expansion. Homozygosity was elevated but not found across large regions, suggesting some past but little current inbreeding. Several regions of the genome were found to be likely under balancing selection, maintained due to heterozygote advantage rather than divergence in emergence timing. These included genes in the circadian clock and DNA methylation pathways. Overall, this genomic work will enable future genetic and epigenetic studies of Callophrys elfin species to clarify the role of introgression in the evolution of these species and the factors that regulate life history variation in eastern pine elfins.
- Genome structure, hybridization, and genetic differentiation through time in Callophrys elfin butterflies
- Uma Knaven
- 0009-0008-9925-8250
- ix, 148 pages
- color illustrations
- List of figures -- List of tables -- Chapter 1. Dissertation introduction -- General background -- Overview of study system -- Dissertation aims -- References -- Chapter 2. Chromosome-level reference genome for the eastern pine elfin, Callophrys niphon -- Introduction -- Methods -- Results -- Discussion -- References -- Chapter 3. Detecting introgression among Callophrys elfins -- Introduction -- Methods -- Results -- Discussion -- References -- Chapter 4. Genetic variation associated with emergence time of Callophrys niphon -- Introduction -- Methods -- Results -- Discussion -- References.
- Includes bibliographical references.
- University of Massachusetts Dartmouth
- Doctor of Philosophy (PHD)
- Integrative Biology
- Department of Biology
- English
- Dissertation
- https://doi.org/10.62791/20601
- 9914540172501301