The Genetics of species differences in the Drosophila virilis group

Thesis (Ph. D.)--University of Rochester. Department of Biology, 2015. "Chapter 1 is a collaboration with Dr. Andrea Sweigart (University of Georgia). Chapter 3 is a collaboration with Dr. Robert Unckless (Cornell University)"--Page vi.My dissertation focuses on two aspects of the genetics of species differences: morphological evolution and speciation. In Chapter 1, I genetically analyze the puparium color difference between members of the virilis group of Drosophila. I used backcross hybrids to map the genomic interval responsible for the difference between Drosophila americana and D. virilis. First, I show that the pupal case color difference is caused by a single gene, dopamine N-acetyltransferase (Dat). This gene encodes an enzyme that is known to play a part in the insect pigmentation pathway. Second, I show that this gene is highly expressed at the onset of pupation in D. americana and D. novamexicana (brown pupae) but not in D. virilis (black pupae) and D. lummei (dark-brown pupae). My results demonstrate that a single gene is almost entirely responsible for a morphological difference between species. In Chapter 2, I turn to the genetic and phenotypic basis of postmating prezygotic reproductive isolation (PMPZ) between D. americana and D. virilis. This species pair shows strong PMPZ isolation, especially when D. americana males mate with D. virilis females. Previous work showed that paternal loci contributing to this incompatibility reside on chromosome 5 (likely carries multiple factors) and chromosome 2 (fixed for a large paracentric inversion). First, I show that PMPZ is due largely to defective sperm storage. Second, I identify regions that carry genes capable of rescuing heterospecific fertilization. I conclude that paternal incompatibility between D. americana males and D. virilis females is underlain by several genes. Finally, I discuss the possible role of candidate accessory gland genes in the mapped chromosomal regions. In Chapter 3, I analyze transcriptomes from male reproductive tissues (accessory glands, testes, and ejaculatory bulb) of virilis group members using RNAseq. First, I identify tissue-biased transcripts and describe enriched functional categories. Second, I compare differences in transcript abundance between species to identify lineage-specific reproductive genes. Finally, I estimate nucleotide substitution rates and perform tests of accelerated codon substitution to identify signatures of positive selection. I conclude that adaptive amino-acid substitutions, expression differences, and gene turnover contribute to divergence among reproductive genes in the D. virilis group