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Abstract
This dissertation includes two parts. The first part, Chapters 2 and 3, address questions about evolution and transcript expression in the plant genus Papaver and relatives within the Ranunculales. Benzylisoquinoline alkaloids (BIAs) are an important class of plant secondary metabolites because they are varied and many are used as pharmaceuticals or are being explored for their pharmaceutical uses. BIAs are primarily produced by the order Ranunculales. A few of these alkaloids are only found in Papaver including some used as pharmaceuticals. In these chapters I infer the phylogenetic relationships of species within the Ranunculales including important representatives of Papaver. I resolve the relationships of major families within the order and explore the gene tree discordance across the phylogeny. RNA-seq analysis were then used to examine the expression of genes in BIA biosynthesis and also to describe gene co-expression networks in Papaver somniferum and Papaver setigerum. Comparative transcriptomics is useful for identifying genes of interest and understanding the evolution of pathways and processes between species. The second part of this dissertation, Chapter 4, acknowledges the importance of graduate training and undergraduate education for scientific progress. Science faculty who see themselves as teachers or have an identity as a teacher may be more likely to adopt evidence-based teaching practices. In this chapter I developed a mechanistic model of the factors that influence professional identity in graduate students. Specifically, I studied factors that hindered or promoted professional identity as a college teacher. Independent teaching experiences, teaching professional development, and teaching mentors contributed to salient and stable teaching identities among doctoral students. Being recognized by faculty as a teacher was also important, but rare. Participants observed that the professional culture of life sciences strongly valued research over teaching, resulting in a sometimes cold and isolating environment for students interested in teaching.