Investigating the molecular basis of adaptation and speciation in divergent populations

Abstract

The creation of biodiversity involves the evolution of new species. Recent trends in the study of speciation have increased the emphasis on the role of ecology in adaptation and the evolution of reproductive isolation. This includes examining the relative contributions of different types of selection, the role of gene flow and the genomic changes that occur during ecological speciation. The search for speciation genes continues, however our growing knowledge of how the genome translates into phenotypes means we should now consider a broader molecular basis of speciation, which includes genetic, transcriptomic and potentially epigenetic variation that contribute to phenotypic variation. This thesis addresses the molecular basis of speciation by using three different complementary methods to examine the early stages of ecological speciation and the evolution of premating reproductive isolation between two incipient species of the cactophilic fly, Drosophila mojavensis. First, the genetic basis was examined through the sequencing of two candidate genes underlying reproductive isolation (Chapter 2). Second, the historical biogeography of population divergence was uncovered using multiple sequenced loci (Chapter 3). Lastly, gene expression across the whole transcriptome associated with phenotypic plasticity and mating success was assessed (Chapter 4). Further, the role of epigenetic imprinting in the population divergence of a freshwater fish, Girardinichthys multiradiatus, was examined through sequencing of a well known gene involved in sexual conflict (Chapter 5). These studies find that uncovering the genetic variation underlying speciation is difficult, especially when there is extensive phenotypic plasticity. Further, gene expression plasticity may play an important role in the evolution of premating isolation, and this includes a role for epigenetic mechanisms of gene expression. Additionally, it is important to assess the demographic scenario of population divergence to put into context the ecological and functional data on divergent groups. Through these studies this thesis examines the genetic, expression and epigenetic variation associated with on-going population divergence, and emphasises the need to consider the potential role of the full range of gene expression changes during ecological speciation.