Abstract
The process of speciation is long and complex, and takes place in multiple stages, with a variety of potential outcomes. Studying lineages at different stages in the speciation process can lend insight into the evolutionary factors that generate and maintain biodiversity. For my dissertation, I used two genomic datasets generated from field-collected DNA samples in two tropical avian systems to examine the early and late stages of the speciation process. I studied the initial stages of speciation in the Amazilia Hummingbird (Amazilia amazilia) subspecies complex. Found across Ecuador and Peru, this species is split into six phenotypically differentiated subspecies. I used a large genotyping-by-sequencing dataset and one mitochondrial marker to assess the phylogeny, population structuring, and gene flow between the subspecies. I found that the six subspecies split into three distinct clades corresponding with geography, with evidence of gene flow across some neighboring subspecies groups. In addition, using environmental data in concordance with the tree, I found that both expansion into new habitats and geographic isolation likely shaped the diversification of subspecies. To study the final stages of speciation—in which two lineages come into secondary contact, I used two species of Zosterops White-eyes, Z. kulambangrae (the Solomons White-eye) and Z. murphyi (the Kolombangara White-eye). These two species are part of the Zosteropidae family of birds, which is known for rapidly speciating yet still becoming geographically widespread (i.e., the paradox of the great speciator). Found on the island of Kolombangara in the Solomon Islands, Z. kulambangrae and Z. murphyi have an elevational contact zone at mid-elevations on the island. Using a large genotyping-by-sequencing dataset and one mitochondrial marker, I found an absence of hybridization and strong reproductive boundaries between the two species, even though the species have only been diverging for approximately two million years. I also explore potential mechanisms for reproductive isolation such as plumage and song. Putting my results into context with other studies using a literature review, I found that in comparison to other avian species pairs, these species have rapidly evolved complete reproductive isolation, which may help to explain the paradox of the great speciator. Finally, I also use the Zosterops genomic dataset to predict current-day population sizes and structuring of both species on the island of Kolombangara, interpreting these population sizes in terms of historical logging and the needs for present-day conservation. Overall, in my dissertation I show the importance of using genomic data in concert with phenotypic and environmental datasets to study different stages of the speciation process. Studying speciation at various time points across different lineages is valuable for understanding how and why species are formed or go extinct, and the mechanisms responsible.