This dissertation explores the systematics, biogeography, and genomics of the gooseneck barnacle Pollicipes elegans, a marine crustacean of the tropical Eastern Pacific. In Chapter 1, I provide a broad framework for my research by introducing and focusing on the long-‐standing debate of the mechanisms behind the latitudinal gradient in species diversity, which provided the initial motivation for using Pollicipes elegans as a model system to study the mechanisms leading to genetic differentiation and speciation in tropical regions. In Chapter 2, I examine the genetic structure, infer patterns of connectivity across the warm tropical waters of the eastern Pacific, and reconstruct the biogeographic history of P. elegans using a statistical phylogeographic framework. Using mitochondrial DNA sequences, I found strong evidence supporting an out-‐of-‐the tropics model of speciation in P. elegans, with a clear phylogeographical break between populations in Mexico and all populations to the south. In Chapter 3, I added sequence data from six nuclear genes to the analysis of genetic structure and found strong evidence for two cryptic species within the nominal P. elegans that likely originated by allopatric speciation across the Central American Gap. I estimated the divergence times between peripheral and central populations, and the effective population sizes of these populations, and found again support for an out-‐of-‐the-‐tropics model of diversification. In Chapter 4, I used RNA sequencing of individuals of P. elegans from each cryptic species to assemble the first transcriptome for this taxon. Data mining of the transcriptome allowed me to identify microsatellite and single nucleotide polymorphism (SNP) markers to be used in future research. Analyses using the SNP dataset revealed evidence for 11 genes under natural selection between the two cryptic species; the genes that were identified may be influenced by spatial variation in sea surface temperature in the tropical eastern Pacific. Lastly, in Chapter 5, I provide guidelines for future studies that should be pursued to help elucidate patterns, mechanisms, and consequences of latitudinal gradients of temperature in the process of allopatric speciation. The phylogeographic and demographic reconstruction for P. elegans in this dissertation provide evidence of the role that temperature may play in population differentiation associated with speciation. The transcriptome analyses provided a large set of genetic markers and a list of candidate genes under selection, a crucial first step in the description of the genetic basis of local thermal adaptation in tropical regions. The information generated in this dissertation provides a novel empirical system that can help elucidate the evolution of tropical diversity and can be used to potentially predict the future impacts of climate change on tropical species
