In this doctoral thesis, I overview the empirical and theoretical consequences of evolution by drift and/or natural selection, as it acts upon lineages during ecological speciation. Then, I outline the evolutionary divergence between two such lineages. To address my questions empirically, I utilize genomic and transcriptomic data applied to a taxon (Daphnia; Crustacea : Cladocera) which serves presently more as an ecological model than a genetic one. I am fortunate to have undertaken the necessary research at the present time and place, where high throughput next-generation sequence data could be generated for and meaningfully applied by a doctoral student for novel purposes. I have had a lot of help.
What follows in this text are an introductory chapter, three data chapters, and a conclusion, concerning the diversity and divergence among North American Daphnia pulex and Daphnia pulicaria. In the second chapter, I use novel data to address their genomic divergence; in the third, their regulatory divergence; and in the fourth, their ongoing hybridization and admixture. Each chapter is written to be submitted as a stand-alone manuscript for publication in a peer-reviewed scientific journal. Herein, their content is presented as a dissertation for the partial fulfillment of the requirements for the degree of Doctor of Philosophy from the University of Notre Dame. Finally, I offer my concluding remarks upon completion of this research, concerning the state of biology as a field, and the immense opportunities that exist going forward.