The Genomic Landscape of the Drosophila nasuta Clade

The Drosophila nasuta clade is a young, rapidly speciating clade comprising approximately a dozen species. They are widely distributed in Asia with populations also found in Hawaii, East Africa, and Oceania; and recently, D. nasuta has been identified as an invasive species in Brazil and is quickly spreading in South America. There are few morphological differences between species; females are indistinguishable between species while males of different species have one of three differentially patterned frons--silvery patches between their eyes--and thoracic banding patterns that are correlated to the frons pattern. There are also varying levels of reproductive isolation between species with over half of interspecific matings producing viable offspring. These characteristics make the D. nasuta clade a promising species group to study speciation./nThe first chapter of this dissertation focuses on the development of genomic resources to study a young, non-model Drosophila species group. The phylogenetic relationship between species of the Drosophila nasuta clade have been inferred multiple times using: mitochondrial genes, X chromosome genes, courtship song, and frons patterning. However, these phylogenies have been inconsistent. We leveraged PacBio SMRT long read sequencing technology to generate a chromosome level genome assembly for D. albomicans, a member of the D. nasuta clade. Sixty eight individuals across the clade were sequenced and phylogenetic analyses on whole genome polymorphism data were used to determine the true species phylogeny. While there were multiple phylogenetic topologies across the genome—likely due to incomplete lineage sorting or widespread introgression—there were two that made up 56% of all topologies and were highly correlated with either the autosomes or X chromosome. We found that the inconsistency between the autosomal and X chromosome topology was due to introgression on the autosomes and, thus, determining that the X chromosome phylogeny reflects the true species relationship in the D. nasuta clade. This chapter highlights the nasuta clade’s potential in studying the evolution of pre- and postzygotic isolation and provides a foundation and genetic resources for such endeavors./nThe second chapter of this dissertation focuses on inversions between species. A hallmark process of speciation is the cessation of gene flow and accumulation of mutations between populations leading up to new species and genomic inversions are one such barrier, especially in the case of radiations like the D. nasuta clade. Inversions prevent recombination and allow for the accumulation of differences between inversion haplotypes. We reconstructed the ancestral karyotype using sequence homology and identified 22 inversions across the phylogeny based on the genome assemblies of D. albomicans, D. nasuta, D. kepulauana, D. sulfurigaster albostrigata, D. sulfurigaster bilimbata, D. sulfurigaster sulfurigaster, and D. pallidifrons generated in chapter 3 of this dissertation. While the overall inversion rate is consistent with previous studies in Drosophila, we find highly variable rates along the different branches of the phylogeny. Additionally, we find higher rates of inversions on the X chromosome relative to autosomes. Upon closer inspection of six autosomal inversions, four of them have repeat sequences associated with them. This implies the importance of ectopic recombination in generating inversions. The characterization of inversions between species in the nasuta clade contributes to future population genetics and functional genomics studies in the species group./nThe third and final chapter of this dissertation looks at transposable elements (TEs) through a phylogenomic framework using the D. nasuta clade--namely how they affect gene expression and how frequently they escape TE repression and expand. We generated six high quality genome assemblies using long read technology for D. nasuta, D. kepulauana, D. s. albostrigata, D. s. bilimbata, D. s. sulfurigaster, and D. pallidifrons and improved on the D. albomicans assembly generated in chapter 1. Leveraging these assemblies, we generated a de novo repeat library for the species group and identified 147 TE families that have expanded in at least one of the species; one TE of note is a DINE element, which has shown multiple instances of expansion with thousands of copies in each genome. Additionally, we find a positive correlation between TEs that have expanded and their expression levels, which follows the expected pattern of suppression escape by the TE. Finally, we find patterns of more extreme gene expression--both elevated and downregulated--associated with TE insertions near or within genes.

Advisor: Bachtrog, Doris