Changes in transcriptional regulatory networks are thought to underlie most morphological change observed across taxa, but the general principles of how such networks change and why remain unknown. While many studies have focused on evolutionary changes in cis-acting components of transcriptional networks (enhancers and transcription factor binding sites), changes in the transcription factor proteins which bind these sites have been mostly overlooked. In this thesis I identify the putative Drosophila transcription factor \her her) as having a highly divergent DNA-binding domain, and examine its DNA-binding profile in two fruitfly species, Drosophila melanogaster and Drosophila pseudoobscura. I find evidence for a large-scale divergence in the distribution of HER binding, as well as a possible difference in DNA-binding preference between these two species. This establishes Drosophila her<\italic> as an excellent system for the study of regulatory evolution through changes in transcription factors.

This dissertation examines the formation of questions in Sm’algyax (Maritime Tsimshianic;ISO: tsi; British Columbia, Alaska) based on new fieldwork. The first part outlines the complex morphosyntactic reflexes of both local and long-distance Ā-movement, including wh-movement, relativization, and focus. Although Sm’algyax exhibits a rigidly ergative pattern in terms of number and person agreement, it shows a unique three-way distinction when extracting core arguments of a predicate. The extraction of an intran- sitive subject, a transitive subject, and a direct object are all marked differently. This reveals an underlying structural distinction between intransitive subjects and transitive objects that is not apparent when these elements remain in their in-situ positions. Moving beyond local movement, I show that long-distance movement is possible and exhibits the same morphosyntactic marking found in local movement in each intermediate clause. This provides clear evidence that cross-clausal movement does not occur in “one fell swoop”, but rather involves intermediate landing spots along the way (Chomsky, 1986, 2000; McCloskey, 2000; Chomsky, 2001; Rackowski & Richards, 2005; Chomsky, 2008; van Urk & Richards, 2015). The second part focuses on a unique set of markers in Sm’algyax—referred to as interrogative clitics—that appear in both wh-questions and polar questions. I show that they are sensitive to a root/non-root clause distinction: they may appear in root/matrix questions, but not embedded questions. Their appearance in matrix questions is sensitive to whether those questions are in some sense canonical questions or not. I analyze the interrogative clitics as operators that appear in a high, peripheral syntactic position, and select for an interrogative clausal complement. Finally, I turn to the linear positioning of the interrogative clitics in the clause, and show that they occupy a typologically rare second-last position. I show that appealing to the syntax, phonology, or a combination of syntax and phonology does not capture their distribution. Instead, I argue that the penultimate linearization implicates a distinct morphological component.