Chapter 1: Divergence, gene flow, and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs My aim in this chapter was to understand the processes driving the origin and maintenance of the geographic distribution of solid-yellow Phyllobates populations in Western Colombia, especially focusing on divergence and gene flow between populations. Using a combination of phylogenetic and spatial population genetic analyses, I characterized the levels of genetic structure and gene flow, as well as the evolutionary relationships between populations. I found high levels of previously unrecognized genetic structure among populations, as well as an even more dynamic evolution of solid-yellow color patterns than previously thought. Furthermore, the data showed a strong signature of short-range gene flow between neighboring population, but not between distant populations. This indicates that gene flow between striped populations may be contributing to their phenotypic similarity, but the same cannot be said for solid-yellow ones. Chapter 2: Disentangling the origin of a color pattern cline In this chapter I focused on the color pattern cline present in the upper San Juan River drainage (see section 1.1 in pg. 2), which connects two recently diverged sister species, one of which is striped and the other solid-yellow. Based on patterns of genetic and phenotypic variation among populations in this area I aimed to understand the biogeographic origin of this color pattern cline. I found patterns consistent with either a recent parapatric range expansion or relatively old ongoing hybridization as the processes generating the cline. I favor the first explanation, as it conforms with our expectation of strong selection on these frogs’ aposematic coloration, which have been backed by recent work on closely related species. Chapter 3: The genetic basis and evolutionary history of color pattern variation in Phyllobates poison frogs Considering the convergent evolution of highly similar color patterns in Phyllobates, which even seem to share a common developmental basis, my last chapter aimed at identifying genomic regions associated with color pattern variation and investigating their evolutionary history to disentangle the genetic processes underlying this instance of convergent evolution. Using genome-wide divergence scans and association analyses I identified several loci associated with color pattern, out of which four stood out as candidate genes involved in color pattern differences. Genetic variation at these loci and their adjacent regions again suggested that introgression has not played a role in the convergent evolution of solid yellow coloration, pointing to independent evolution of these species’ color patterns.