Interspecific Hybrids

The regulation of gene expression is essential for organismal form, function, and fitness. Complex organismal development from zygote to adult requires finely tuned expression of genes in space, time, and abundance. Proper expression of genes is also required for most other aspects of physiology and function. Even minor changes in gene expression have the potential to significantly impact phenotypes (e.g., Oleksiak et al., 2005; Cooley et al., 2012). Despite the central role that gene expression plays in converting genotypes into phenotypes, abundant variation in gene expression exists within and between species. While not all of this variation is expected to impact phenotypes, changes in gene expression have been shown to contribute to the evolution of diverse traits, including bat wings (Cretekos et al., 2008), turtle shells (Moustakas, 2008), stickleback spines (Shapiro et al., 2004; Chan et al., 2010), corn kernels (Clark et al., 2006), beak morphology in Darwin’s finches (Abzhanov et al., 2004), and body color differences within and between species of Drosophila, butterfly, and mice (Wittkopp et al., 2003; Kronforst et al., 2012). Genetic changes underlying interspecific expression differences may also contribute to speciation by causing hybrid incompatibilities (e.g., Maheshwari & Barbash, 2012). Gene expression begins with transcription, and the molecular mechanisms controlling when, where, and how frequently a DNA sequence encoding a gene product is transcribed into RNA are much better understood than those responsible for posttranscriptional regulation. Fundamentally, transcription is controlled by interactions between cis-regulatory DNA and trans-acting RNA and proteins. cis-Regulatory sequences include the basal promoter located 5′ of the transcription start site of each gene upon which the multiprotein RNA polymerase holoenzyme complex of transacting factors assembles. Alone, this complex produces “basal” levels of RNA transcripts. These levels are often modified in multicellular eukaryotes by additional cis-regulatory elements located in noncoding sequences, 5′ or 3′ of the transcription start site, which are known as enhancers. These enhancers bind to sets of trans-acting transcription factors that act combinatorially to enhance or repress transcription. Interactions between transcription factor complexes assembled on enhancers and on the basal promoter occur through changes in DNA shape (looping) and/or other molecular mechanisms (reviewed in Wray et al., 2003) (Figure 3.1A). Chromatin structure and DNA sequences